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1.  Feasibility of one-shot-per-crystal structure determination using Laue diffraction 
Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals.
Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.
PMCID: PMC2803125  PMID: 20057043
Laue diffraction; microcrystallography; X-ray optics
2.  Structure of the Taz2 domain of p300: insights into ligand binding 
The crystal structure of the Taz2 zinc-finger domain of the human p300 transcriptional coactivator was determined using the anomalous diffraction signal of the bound Zn ions. Crystal contacts suggested a possible novel mode of Taz2–peptide ligand interactions.
CBP and its paralog p300 are histone acetyl transferases that regulate gene expression by interacting with multiple transcription factors via specialized domains. The structure of a segment of human p300 protein (residues 1723–1836) corresponding to the extended zinc-binding Taz2 domain has been investigated. The crystal structure was solved by the SAD approach utilizing the anomalous diffraction signal of the bound Zn ions. The structure comprises an atypical helical bundle stabilized by three Zn ions and closely resembles the solution structures determined previously for shorter peptides. Residues 1813–1834 from the current construct form a helical extension of the C-terminal helix and make extensive crystal-contact interactions with the peptide-binding site of Taz2, providing additional insights into the mechanism of the recognition of diverse transactivation domains (TADs) by Taz2. On the basis of these results and molecular modeling, a hypothetical model of the binding of phosphorylated p53 TAD1 to Taz2 has been proposed.
PMCID: PMC2789004  PMID: 19966416
zinc-finger proteins; anomalous diffraction; protein recognition; transcription regulation
3.  A case of structure determination using pseudosymmetry 
When properly applied, pseudosymmetry can be used to improve crystallographic phases through averaging and to facilitate crystal structure determination.
Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third of the monoclinic reflections obeyed pseudo-orthorhombic P21212 symmetry similar to that of the wild-type crystals and could be indexed and processed in this space group. The pseudo-orthorhombic and monoclinic unit cells were related by the following vector operations: a m = b o − c o, b m = a o and c m = −2c o − b o. The pseudo-orthorhombic subset of data produced good SAD phases, leading to structure determination with one monomer in the asymmetric unit. Subsequently, the structure of the Mac-1 mutant in the monoclinic form was determined by molecular replacement, which showed six molecules forming three translationally related dimers aligned along the (1 0 1) diagonal. Knowing the geometric relationship between the pseudo-orthorhombic and the monoclinic unit cells, all six molecules can be generated in the monoclinic unit cell directly without the use of molecular replacement. The current case provides a successful example of the use of pseudosymmetry as a powerful phase-averaging method for structure determination by anomalous diffraction techniques. In particular, a structure can be solved in a higher pseudosymmetry subcell in which an NCS operator becomes a crystallographic operator. The geometrical relationships between the subcell and parental cell can be used to generate a complete molecular representation of the parental asymmetric unit for refinement.
PMCID: PMC2789005  PMID: 19966420
pseudosymmetry; structure determination; cysteine proteases; Mac-1
4.  The effect of protein–precipitant interfaces and applied shear on the nucleation and growth of lysozyme crystals 
The nucleation of lysozyme in microbatch experiments was linked to the formation of protein–precipitant interfaces. The use of oscillatory shear allowed decreasing the nucleation rate and extending the growth period for lysozyme crystals, presumably through the control of the number of interfaces and removal of impurities or defects.
This paper is concerned with the effect of protein–precipitant interfaces and externally applied shear on the nucleation and growth kinetics of hen egg-white lysozyme crystals. The early stages of microbatch crystallization of lysozyme were explored using both optical and confocal fluorescence microscopy imaging. Initially, an antisolvent (precipitant) was added to a protein drop and the optical development of the protein–precipitant interface was followed with time. In the presence of the water-soluble polymer poly(ethylene glycol) (PEG) a sharp interface was observed to form immediately within the drop, giving an initial clear separation between the lighter protein solution and the heavier precipitant. This interface subsequently became unstable and quickly developed within a few seconds into several unstable ‘fingers’ that represented regions of high concentration-gradient interfaces. Confocal microscopy demonstrated that the subsequent nucleation of protein crystals occurred preferentially in the region of these interfaces. Additional experiments using an optical shearing system demonstrated that oscillatory shear significantly decreased nucleation rates whilst extending the growth period of the lysozyme crystals. The experimental observations relating to both nucleation and growth have relevance in developing efficient and reliable protocols for general crystallization procedures and the controlled crystallization of single large high-quality protein crystals for use in X-ray crystallo­graphy.
PMCID: PMC2777168  PMID: 19923710
lysozyme crystallization; nucleation; growth; shear; interfaces; instabilities; concentration gradients
5.  Protein flexibility: coordinate uncertainties and interpretation of structural differences 
Criteria for the interpretability of coordinate differences and a new method for identifying rigid-body motions and nonrigid deformations in protein conformational changes are developed and applied to functionally induced and crystallization-induced conformational changes.
Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent ‘noise’, showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations may be doubtful or erroneous. The use of uncertainty thresholds, DDMs, the newly introduced CDDMs (contact distance difference matrices) and a novel simple rotation algorithm allows a more meaningful classification and description of protein motions, distinguishing between various rigid-fragment motions and nonrigid conformational deformations. It is also shown that half of 75 pairs of identical molecules, each from the same asymmetric crystallo­graphic cell, exhibit coordinate differences that range from just outside the coordinate uncertainty threshold to the full magnitude of large functional movements. Thus, crystallization might often induce protein conformational changes that are comparable to those related to or induced by the protein function.
PMCID: PMC2777169  PMID: 19923711
bioinformatics; computation; validation; molecular machines; rigid parts
6.  Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein 
Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing of the trimeric ebolavirus glycoprotein are described.
The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008 ▶), Nature (London), 454, 177–182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glyco­protein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the proper sequence register was confirmed by building alternate sequences using N-linked glycan sites as anchors and secondary-structural predictions.
PMCID: PMC2777170  PMID: 19923712
glycoproteins; structure determination; difficult structures; antibody complexes; viral proteins; human proteins; tactics to improve diffraction; techniques for phase determination; deglycosylation; model building
7.  A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase 
The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine.
Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k cat. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As pre­dicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.
PMCID: PMC3089011  PMID: 19923719
GMC oxidoreductases; site-directed mutagenesis; hydrophobic tunnel; flavoproteins
8.  Overproduction, purification and structure determination of human dual-specificity phosphatase 14 
The crystal structure of human dual-specificity phosphatase 14, DUSP14 (MKP6), in complex with a phosphate ion has been determined and refined to 1.88 Å resolution.
Dual-specificity phosphatases (DUSPs) are enzymes that participate in the regulation of biological processes such as cell growth, differentiation, transcription and metabolism. A number of DUSPs are able to dephosphorylate phosphoryl­ated serine, threonine and tyrosine residues on mitogen-activated protein kinases (MAPKs) and thus are also classified as MAPK phosphatases (MKPs). As an increasing number of DUSPs are being identified and characterized, there is a growing need to understand their biological activities at the molecular level. There is also significant interest in identifying DUSPs that could be potential targets for drugs that modulate MAPK-dependent signaling and immune responses, which have been implicated in a variety of maladies including cancer, infectious diseases and inflammatory disorders. Here, the overproduction, purification and crystal structure at 1.88 Å resolution of human dual-specificity phosphatase 14, DUSP14 (MKP6), are reported. This structural information should accelerate the study of DUSP14 at the molecular level and may also accelerate the discovery and development of novel therapeutic agents.
PMCID: PMC2748964  PMID: 19770498
dual-specificity phosphatases; MAPK phosphatases; DUSP14; MKP6
9.  A multivariate likelihood SIRAS function for phasing and model refinement 
The application of a multivariate likelihood function to a single isomorphous replacement with anomalous scattering experiment improves phasing and automated model building with iterative refinement in the test cases shown.
A likelihood function based on the multivariate probability distribution of all observed structure-factor amplitudes from a single isomorphous replacement with anomalous scattering experiment has been derived and implemented for use in substructure refinement and phasing as well as macromolecular model refinement. Efficient calculation of a multidimensional integration required for function evaluation has been achieved by approximations based on the function’s properties. The use of the function in both phasing and protein model building with iterative refinement was essential for successful automated model building in the test cases presented.
PMCID: PMC2748965  PMID: 19770502
multivariate normal probability distribution; single isomorphous replacement with anomalous scattering; experimental phasing; direct incorporation of prior phase information
10.  electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation 
A new software system for automated ligand coordinate and restraint generation is presented.
The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses simple and fast quantum-chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow the attainment of a number of diverse goals including geometry optimization and generation of restraints.
PMCID: PMC2748967  PMID: 19770504
ligands; coordinates; restraints; Python; object-oriented programming
11.  A neutron crystallographic analysis of T6 porcine insulin at 2.1 Å resolution 
The charge balance and hydrogen-bonding network at the core of the insulin T6 hexamer have been investigated by neutron diffraction analysis at 2.1 Å resolution.
Neutron diffraction data for T6 porcine insulin were collected to 2.1 Å resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structure was refined to a residual of 0.179. The hydrogen-bonding network of the central core of the hexamer was observed and the charge balance between positively charged Zn ions and their surrounding structure was interpreted by considering the protonation and/or deprotonation states and interactions of HisB10, water and GluB13. The observed double conformation of GluB13 was essential to interpreting the charge balance and could be compared with the structure of a dried crystal of T6 human insulin at 100 K. Differences in the dynamic behaviour of the water molecules coordinating the upper and lower Zn ions were observed and interpreted. The hydrogen bonds in the insulin molecules, as well as those involving HisB10 and GluB13, are discussed. The hydrogen/deuterium (H/D) exchange ratios of the amide H atoms of T6 porcine insulin in crystals were obtained and showed that regions highly protected from H/D exchange are concentrated in the centre of a helical region of the B chains. From the viewpoint of soaking time versus H/D-exchange ratios, the amide H atoms can be classified into three categories.
PMCID: PMC2756163  PMID: 19770501
T6 insulin; neutron crystallography; protonation; charge balance; H/D exchange; hydrogen bonds
12.  A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity 
The crystal structure of tear lipocalin determined in space group P21 revealed large structural deviations from the previously solved X-ray structure in space group C2, especially in the loop region and adjoining parts of the β-barrel which give rise to the ligand-binding site. These findings illustrate a novel mechanism for promiscuity in ligand recognition by the lipocalin protein family.
Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P21 crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-­barrel and (iii) in the extended C-terminal segment, which is attached to the β-­barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family.
PMCID: PMC2756164  PMID: 19770509
apolipoprotein D; β-barrel; 1,4-butanediol; induced fit; tear lipocalin; von Ebner’s gland protein
13.  Structure of d-alanine-d-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme–ligand interactions 
The structures of five forms of d-alanine-d-alanine ligase from T. thermophilus HB8 showed a cumulative conformational change of the molecular structure through the induced rotation of the central domain in concert with a local conformational change of three loops. The active-site structures shed light on the catalytic mechanism and the roles of the conformational change.
d-Alanine-d-alanine ligase (Ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. The enzyme catalyzes the condensation of two d-­Ala molecules using ATP to produce d-Ala-d-Ala, which is the terminal peptide of a peptidoglycan monomer. The structures of five forms of the enzyme from Thermus thermophilus HB8 (TtDdl) were determined: unliganded TtDdl (2.3 Å resolution), TtDdl–adenylyl imidodiphosphate (2.6 Å), TtDdl–ADP (2.2 Å), TtDdl–ADP–d-Ala (1.9 Å) and TtDdl–ATP–d-Ala-d-Ala (2.3 Å). The central domain rotates as a rigid body towards the active site in a cumulative manner in concert with the local conformational change of three flexible loops depending upon substrate or product binding, resulting in an overall structural change from the open to the closed form through semi-open and semi-closed forms. Reaction-intermediate models were simulated using TtDdl-complex structures and other Ddl structures previously determined by X-ray methods. The catalytic process accompanied by the cumulative conformational change has been elucidated based on the intermediate models in order to provide new insights regarding the details of the catalytic mechanism.
PMCID: PMC2756165  PMID: 19770507
d-alanine-d-alanine ligase; Thermus thermophilus HB8; catalytic mechanism; conformational change
14.  End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures 
New classes of helix–helix interactions in protein structures are reported in which interactions only occur at the terminal regions or between the terminal region of one helix and the middle region of another helix.
Helix–helix interactions are important for the structure, stability and function of α-helical proteins. Helices that either cross in the middle or show extensive contacts between each other, such as coiled coils, have been investigated in previous studies. Interactions between two helices can also occur only at the terminal regions or between the terminal region of one helix and the middle region of another helix. Examples of such helix pairs are found in aquaporin, H+/Cl− transporter and Bcl-2 proteins. The frequency of the occurrence of such ‘end-to-end’ (EE) and ‘end-to-middle’ (EM) helix pairs in protein structures is not known. Questions regarding the residue preferences in the interface and the mode of interhelical interactions in such helix pairs also remain unanswered. In this study, high-resolution structures of all-α proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N–N, N–C, C–C, N–MID and C–MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue pro­pensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-­terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their preferences for occurring in the interface of EE and EM helix pairs. In contrast to interacting non-EE/EM helix pairs, helices in EE and EM pairs are farther apart. In these helix pairs, residues with large surface area/volume and longer side chains are preferred in the interfacial region.
PMCID: PMC2756166  PMID: 19770500
helix-packing interactions; helix–helix interfaces; residue surface areas; side-chain lengths; interhelical hydrophobic contacts; interhelical distances
15.  On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination 
The combination of molecular replacement and single-wavelength anomalous diffraction improves the performance of automated structure determination with Auto-Rickshaw.
A combination of molecular replacement and single-wavelength anomalous diffraction phasing has been incorporated into the automated structure-determination platform Auto-Rickshaw. The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building. The improvement over the standard SAD or MR approaches is illustrated by ten test cases taken from the JCSG diffraction data-set database. Poor MR or SAD phases with phase errors larger than 70° can be improved using the described procedure and a large fraction of the model can be determined in a purely automatic manner from X-ray data extending to better than 2.6 Å resolution.
PMCID: PMC2756167  PMID: 19770506
automated structure determination; molecular replacement; single-wavelength anomalous diffraction
16.  Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity 
APS kinase from Thiobacillus denitrificans contains an inactive N-terminal ATP sulfurylase domain. The structure presented unveils the first hexameric assembly for an APS kinase, and reveals that structural changes in the N-terminal domain disrupt the ATP sulfurylase active site thus prohibiting activity.
The Tbd_0210 gene of the chemolithotrophic bacterium Thiobacillus denitrificans is annotated to encode a 60.5 kDa bifunctional enzyme with ATP sulfurylase and APS kinase activity. This putative bifunctional enzyme was cloned, expressed and structurally characterized. The 2.95 Å resolution X-ray crystal structure reported here revealed a hexa­meric assembly with D 3 symmetry. Each subunit contains a large N-terminal sulfurylase-like domain and a C-terminal APS kinase domain reminiscent of the two-domain fungal ATP sulfurylases of Penicillium chrysogenum and Saccharo­myces cerevisiae, which also exhibit a hexameric assembly. However, the T. denitrificans enzyme exhibits numerous structural and sequence differences in the N-terminal domain that render it inactive with respect to ATP sulfurylase activity. Surprisingly, the C-terminal domain does indeed display APS kinase activity, indicating that this gene product is a true APS kinase. Therefore, these results provide the first structural insights into a unique hexameric APS kinase that contains a nonfunctional ATP sulfurylase-like domain of unknown function.
PMCID: PMC2756168  PMID: 19770499
APS kinases; adenylylsulfate kinases; ATP sulfurylases; sulfate metabolism; nucleotide kinase; Thiobacillus denitrificans
17.  Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers 
A new algorithm that automatically models discrete heterogeneity in X-ray data demonstrates that the variability observed at high resolution can be adequately represented by including correlated structural features in protein models. The algorithm is based on simultaneous exploration of a very large number of alternative interpretations of electron-density maps.
The native state of a protein is regarded to be an ensemble of conformers, which allows association with binding partners. While some of this structural heterogeneity is retained upon crystallization, reliably extracting heterogeneous features from diffraction data has remained a challenge. In this study, a new algorithm for the automatic modelling of discrete hetero­geneity is presented. At high resolution, the authors’ single multi-conformer model, with correlated structural features to represent heterogeneity, shows improved agreement with the diffraction data compared with a single-conformer model. The model appears to be representative of the set of structures present in the crystal. In contrast, below 2 Å resolution representing ambiguous electron density by correlated multi-conformers in a single model does not yield better agreement with the experimental data. Consistent with previous studies, this suggests that variability in multi-conformer models at lower resolution levels reflects uncertainty more than co­ordinated motion.
PMCID: PMC2756169  PMID: 19770508
heterogeneity; modeling; multi-conformers
18.  Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment 
The crystal structure of PCNA from the halophilic archaeon H. volcanii reveals specific features of the charge distribution on the protein surface that reflect adaptation to a high-salt environment and suggests a different type of interaction with DNA in halophilic PCNAs.
The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (R free = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells.
PMCID: PMC2756170  PMID: 19770505
PCNA–DNA interactions; sliding clamps; halophilic environment
19.  Rotational order–disorder structure of fluorescent protein FP480 
An analysis of the rotational order–disorder structure of fluorescent protein FP480 is presented.
In the last decade, advances in instrumentation and software development have made crystallography a powerful tool in structural biology. Using this method, structural information can now be acquired from pathological crystals that would have been abandoned in earlier times. In this paper, the order–disorder (OD) structure of fluorescent protein FP480 is discussed. The structure is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, namely rotated 90° with respect to each other around the crystal c axis, with tetramer axes coincident with crystallo­graphic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates a rotational OD structure with statistically averaged I422 symmetry, although the presence of very weak and diffuse additional reflections suggests that the randomness is only approximate.
PMCID: PMC2733879  PMID: 19690368
order–disorder structures; rotational order–disorder; fluorescent proteins
20.  Automatic implementation of precise grid screens: the four-corners method 
An efficient and accurate method has been developed for the preparation of the customized crystallization grid screens employed in protein crystallizations.
Crystallization trials can be designed as a systematic gradient of the concen­tration of key reagents and/or pH centered on the original conditions. While the concept of the grid screen is simple, its implementation is tedious and difficult by hand. A procedure has been developed for preparing crystallization grid screens that is both efficient and achieves high accuracy because it relies on a limited number of solutions that are carefully prepared by hand. The ‘four-corners’ approach to designing grid screens uses the minimum and maximum concen­trations of the components being varied in the grid screen as the sole stock solutions. For an N-dimensional grid only 2N corner solutions require detailed preparation, making the screens efficient. Furthermore, by keeping the concentrations as tight as possible to the grid, the potential impact of pipette errors is minimized, creating a highly precise screen.
PMCID: PMC2733884  PMID: 19690378
crystallization; grid screens; pH; robotics
21.  To scavenge or not to scavenge: that is the question 
Analysis of a series of diffraction data sets measured from several native as well as nicotinic acid-soaked crystals of trypsin suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation at 100 K.
Analysis of a series of diffraction data sets measured from four native as well as four nicotinic acid-soaked crystals of trypsin at 100 K shows a high variability in radiation-sensitivity among individual crystals for both nicotinic acid-soaked and native crystals. The level of radiation-sensitivity and the extent of its variability is statistically indistinguishable between the two conditions. This suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation. This is in contrast to previous results [Kauffmann et al. (2006 ▶), Structure, 14, 1099–1105] where only one crystal specimen was used for each condition (native and nicotinic acid-soaked).
PMCID: PMC2733885  PMID: 19690379
protein crystallography; radiation damage; scavengers; nicotinic acid
22.  Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius  
Here, the crystal structure of an endoglucanase, Cel9A, from Alicyclobacillus acidocaldarius (Aa_Cel9A) is reported which displays a modular architecture composed of an N-terminal Ig-like domain connected to the catalytic domain. This paper describes the overall structure and the detailed contacts between the two modules.
The production of biofuels using biomass is an alternative route to support the growing global demand for energy and to also reduce the environmental problems caused by the burning of fossil fuels. Cellulases are likely to play an important role in the degradation of biomass and the production of sugars for subsequent fermentation to fuel. Here, the crystal structure of an endoglucanase, Cel9A, from Alicyclobacillus acidocaldarius (Aa_Cel9A) is reported which displays a modular architecture composed of an N-terminal Ig-like domain connected to the catalytic domain. This paper describes the overall structure and the detailed contacts between the two modules. Analysis suggests that the inter­action involving the residues Gln13 (from the Ig-­like module) and Phe439 (from the catalytic module) is important in maintaining the correct conformation of the catalytic module required for protein activity. Moreover, the Aa_Cel9A structure shows three metal-binding sites that are associated with the thermostability and/or substrate affinity of the enzyme.
PMCID: PMC2714717  PMID: 19622857
endoglucanases; thermoacidophiles; cellulases; biofuels
23.  Structure of ristocetin A in complex with a bacterial cell-wall mimetic 
The crystal structure of the complex between ristocetin A and the cell-wall peptide mimetic N-acetyl-lysine-d-alanine-d-alanine has been solved. Structural details explaining the anticooperativity of the antibiotic have been identified.
Antimicrobial drug resistance is a serious public health problem and the development of new antibiotics has become an important priority. Ristocetin A is a class III glycopeptide antibiotic that is used in the diagnosis of von Willebrand disease and which has served as a lead compound for the development of new antimicrobial therapeutics. The 1.0 Å resolution crystal structure of the complex between ristocetin A and a bacterial cell-wall peptide has been determined. As is observed for most other glycopeptide antibiotics, it is shown that ristocetin A forms a back-to-back dimer containing concave binding pockets that recognize the cell-wall peptide. A comparison of the structure of ristocetin A with those of class I glycopeptide antibiotics such as vancomycin and balhimycin identifies differences in the details of dimerization and ligand binding. The structure of the ligand-binding site reveals a likely explanation for ristocetin A’s unique anti­cooperativity between dimerization and ligand binding.
PMCID: PMC2714720  PMID: 19622867
glycopeptide antibiotics; vancomycin; antimicrobial resistance
24.  What can we learn by computing 13Cα chemical shifts for X-ray protein models? 
The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution.
The room-temperature X-ray structures of ubiquitin (PDB code 1ubq) and of the RNA-binding domain of nonstructural protein 1 of influenza A virus (PDB code 1ail) solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13Cα chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13Cα chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13Cα chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13Cα chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13Cα chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with accuracy as good as the PDB structure. Therefore, generation of an ensemble is a necessary step to determine whether or not a single structure is sufficient for an accurate representation of both experimental X-ray data and observed 13Cα chemical shifts in solution.
PMCID: PMC2703576  PMID: 19564690
13C chemical shifts
25.  Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin 
Complications to molecular replacement resulting from a poor starting search model, pseudosymmetry, twinning and a high copy number in the asymmetric unit made the determination of the structure of D. desulfuricans (ATCC 29577) flavodoxin in two crystal forms challenging.
The crystal structure of oxidized flavodoxin from Desulfo­vibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0 Å resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (−h, −k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.
PMCID: PMC2685730  PMID: 19465766
flavodoxins; pseudosymmetry; twinning; high copy number; molecular replacement

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