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1.  Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase 
A case of imperfect pseudo-merohedral twinning in monoclinic crystals of fungal fatty acid synthase is discussed. A space-group transition during crystal dehydration resulted in a Moiré pattern-like interference of the twinned diffraction patterns.
The recent high-resolution structures of fungal fatty acid synthase (FAS) have provided new insights into the principles of fatty acid biosynthesis by large multifunctional enzymes. The crystallographic phase problem for the 2.6 MDa fungal FAS was initially solved to 5 Å resolution using two crystal forms from Thermomyces lanuginosus. Monoclinic crystals in space group P21 were obtained from orthorhombic crystals in space group P212121 by dehydration. Here, it is shown how this space-group transition induced imperfect pseudo-merohedral twinning in the monoclinic crystal, giving rise to a Moiré pattern-like interference of the two twin-related reciprocal lattices. The strategy for processing the twinned diffraction images and obtaining a quantitative analysis is presented. The twinning is also related to the packing of the molecules in the two crystal forms, which was derived from self-rotation function analysis and molecular-replacement solutions using a low-resolution electron microscopy map as a search model.
doi:10.1107/S0907444909000778
PMCID: PMC2631638  PMID: 19171964
imperfect pseudo-merohedral twinning; fungal fatty acid synthase
2.  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.
doi:10.1107/S0907444909010075
PMCID: PMC2685730  PMID: 19465766
flavodoxins; pseudosymmetry; twinning; high copy number; molecular replacement
3.  Crystallization and preliminary X-ray diffraction analysis of Salmonella typhi PilS 
Crystals of the recombinant native and selenomethionine PilS protein belong to the orthorhombic space group P21212, with unit-cell parameters a = 77.88, b = 114.53, c = 31.75 Å. The structure will be solved using the MAD method.
The structure determination of PilS, a type IV pilin, by X-ray crystallography is reported. The recombinant protein from Salmonella typhi was overexpressed, purified and crystallized. The crystals belong to space group P21212, with unit-cell parameters a = 77.88, b = 114.53, c = 31.75 Å. The selenomethionine derivative of the PilS protein was overexpressed, purified and crystallized in the same space group. Data sets have been collected to 2.1 Å resolution from the selenomethionine-derivative crystal using synchrotron radiation for multiwavelength anomalous dispersion (MAD) phasing.
doi:10.1107/S174430910603661X
PMCID: PMC2225195  PMID: 17012803
PilS; Salmonella typhi; type IV pilin
4.  Surprises and pitfalls arising from (pseudo)symmetry 
The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.
It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new notation for space groups in unusual settings is introduced. The main concepts are illustrated with several examples from the literature and the Protein Data Bank.
doi:10.1107/S090744490705531X
PMCID: PMC2394827  PMID: 18094473
pathology; twinning; pseudosymmetry
5.  The pseudosymmetric structure of bis­(pentane-1,5-diaminium) iodide tris­(triiodide) 
The asymmetric unit of the title compound, [H3N(CH2)5NH3]2I[I3]3 or 2C5H16N2 2+·3I3 −·I−, consists of two crystallographically independent pentane-1,5-diaminium dications and two triiodide anions in general positions besides two additional triiodide and two iodide anions located on twofold axes. The compound crystallizes in the centrosymmetric monoclinic space group P2/n. The structure refinement was handicapped by the pseudosymmetry (pseudo-centering) of the structure and by twinning. The crystal structure is composed of two alternate layers, which differ in their arrangement of the pentane-1,5-diaminium dications and the iodide/triiodide anions and which are connected via weak to medium–strong N—H⋯I hydrogen bonds, constructing a complex hydrogen-bonded network.
doi:10.1107/S1600536812014420
PMCID: PMC3344470  PMID: 22590232
6.  Detection and correction of underassigned rotational symmetry prior to structure deposition 
An X-ray structural model can be reassigned to a higher symmetry space group using the presented framework if its noncrystallographic symmetry operators are close to being exact crystallographic relationships. About 2% of structures in the Protein Data Bank can be reclassified in this way.
Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit.
doi:10.1107/S0907444910001502
PMCID: PMC2865365  PMID: 20445225
underassigned rotational symmetry; LABELIT; validation
7.  Crystallization and initial X-ray diffraction studies of the flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from the soil bacterium Paracoccus denitrificans  
The flavin-dependent enzyme FerB from P. denitrificans has been purified and both native and SeMet-substituted FerB have been crystallized. The two variants crystallized in two different crystallographic forms belonging to the monoclinic space group P21 and the orthorhombic space group P21212, respectively. X-ray diffraction data were collected to 1.75 Å resolution for both forms.
The flavin-dependent enzyme FerB from Paracoccus denitrificans reduces a broad range of compounds, including ferric complexes, chromate and most notably quinones, at the expense of the reduced nicotinamide adenine dinucleotide cofactors NADH or NADPH. Recombinant unmodified and SeMet-substituted FerB were crystallized under similar conditions by the hanging-drop vapour-diffusion method with microseeding using PEG 4000 as the precipitant. FerB crystallized in several different crystal forms, some of which diffracted to approximately 1.8 Å resolution. The crystals of native FerB belonged to space group P21, with unit-cell parameters a = 61.6, b = 110.1, c = 65.2 Å, β = 118.2° and four protein molecules in the asymmetric unit, whilst the SeMet-substituted form crystallized in space group P21212, with unit-cell parameters a = 61.2, b = 89.2, c = 71.5 Å and two protein molecules in the asymmetric unit. Structure determination by the three-wavelength MAD/MRSAD method is now in progress.
doi:10.1107/S1744309110005099
PMCID: PMC2852337  PMID: 20383015
flavoenzymes; quinone reductases; Paracoccus denitrificans
8.  Tetartohedral twinning could happen to you too 
A review of published tetartohedrally twinned macromolecular structures is presented, together with details of the recent structure determination of triclinic tetartohedrally twinned crystals of human complement factor I.
Tetartohedral crystal twinning is discussed as a particular case of (pseudo)merohedral twinning when the number of twinned domains is four. Tetartohedrally twinned crystals often possess pseudosymmetry, with the rotational part of the pseudo­symmetry operators coinciding with the twinning operators. Tetartohedrally twinned structures from the literature are reviewed and the recent structure determination of tetartohedrally twinned triclinic crystals of human complement factor I is discussed.
doi:10.1107/S0907444912006737
PMCID: PMC3322600  PMID: 22505261
tetartohedral twinning
9.  Crystallization and preliminary X-ray analysis of the O-carbamoyltransferase NovN from the novobiocin-biosynthetic cluster of Streptomyces spheroides  
Crystals of NovN, an O-carbamoyltransferase from S. spheroides, were obtained in monoclinic and orthorhombic forms and native X-ray data were recorded to a maximum of 2.3 Å resolution.
Crystals of recombinant NovN, an O-carbamoyltransferase from Streptomyces spheroides, were grown by vapour diffusion. The protein crystallized in two different crystal forms. Crystal form I belonged to space group C2 and native data were collected to 2.9 Å resolution in-house. Crystal form II had I-centred orthorhombic symmetry and native data were recorded to a resolution of 2.3 Å at a synchrotron. NovN catalyses the final step in the biosynthesis of the aminocoumarin antibiotic novobiocin that targets the essential bacterial enzyme DNA gyrase.
doi:10.1107/S1744309108030145
PMCID: PMC2581686  PMID: 18997325
NovN; O-carbamoyltransferases; Streptomyces; novobiocin; antibiotic biosynthesis
10.  Crystallization and preliminary crystallographic analysis of mouse peroxiredoxin II with significant pseudosymmetry 
Mouse peroxiredoxin II was crystallized in an orthorhombic space group and native X-ray diffraction data were collected.
Peroxiredoxin II was cloned from mouse B cells into pCold 1 expression vector and produced as a His-tagged recombinant protein in Escherichia coli. A ring form was isolated by gel filtration. A crystal obtained by the sitting-drop vapour-diffusion method diffracted to 1.77 Å resolution at 100 K. The crystal belonged to space group P21212, with unit-cell parameters a = 117.4, b = 133.9, c = 139.1 Å. The asymmetric unit is expected to contain six dimers of peroxiredoxin II, with a corresponding solvent content of 39.3%. Peaks in the native Patterson function together with pseudo-systematic absences suggested that the crystals suffered from severe translational pseudosymmetry.
doi:10.1107/S1744309110003684
PMCID: PMC2833056  PMID: 20208180
peroxiredoxins; pseudosymmetry
11.  Structure of 3-oxoacyl-(acyl-carrier protein) synthase II from Thermus thermophilus HB8 
The crystal structure of 3-oxoacyl-(acyl-carrier protein) synthase II from T. thermophilus HB8 has been determined at 2.0 Å resolution and compared with the structures of β-keto-ACP synthases from other sources.
The β-ketoacyl-(acyl carrier protein) synthases (β-keto-ACP synthases; KAS) catalyse the addition of two-carbon units to the growing acyl chain during the elongation phase of fatty-acid synthesis. As key regulators of bacterial fatty-acid synthesis, they are promising targets for the development of new antibacterial agents. The crystal structure of 3-oxoacyl-ACP synthase II from Thermus thermophilus HB8 (TtKAS II) has been solved by molecular replacement and refined at 2.0 Å resolution. The crystal is orthorhombic, space group P21212, with unit-cell parameters a = 72.07, b = 185.57, c = 62.52 Å, and contains one homodimer in the asymmetric unit. The subunits adopt the well known α-β-α-β-α thiolase fold that is common to ACP synthases. The structural and sequence similarities of TtKAS II to KAS I and KAS II enzymes of known structure from other sources support the hypothesis of comparable enzymatic activity. The dimeric state of TtKAS II is important to create each fatty-acid-binding pocket. Closer examination of KAS structures reveals that compared with other KAS structures in the apo form, the active site of TtKAS II is more accessible because of the ‘open’ conformation of the Phe396 side chain.
doi:10.1107/S1744309108010336
PMCID: PMC2376401  PMID: 18453702
acyl-carrier protein synthases; homodimers
12.  Crystallization and preliminary crystallographic analysis of a family 43 β-d-xylosidase from Geobacillus stearothermophilus T-6 
The crystallization and preliminary X-ray analysis of a β-d-xylosidase from G. stearothermophilus T-6, a family 43 glycoside hydrolase, is described. Native and catalytic inactive mutants of the enzymes were crystallized in two different space groups, orthorhombic P21212 and tetragonal P41212 (or the enantiomorphic space group P43212), using a sensitive cryoprotocol. The latter crystal form diffracted X-rays to a resolution of 2.2 Å.
β-d-Xylosidases (EC 3.2.1.37) are hemicellulases that cleave single xylose units from the nonreducing end of xylooligomers. In this study, the crystallization and preliminary X-ray analysis of a β-d-xylosidase from Geobacillus stearothermophilus T-6 (XynB3), a family 43 glycoside hydrolase, is described. XynB3 is a 535-amino-acid protein with a calculated molecular weight of 61 891 Da. Purified recombinant native and catalytic inactive mutant proteins were crystallized and cocrystallized with xylobiose in two different space groups, P21212 (unit-cell parameters a = 98.32, b = 99.36, c = 258.64 Å) and P41212 (or the enantiomorphic space group P43212; unit-cell parameters a = b = 140.15, c = 233.11 Å), depending on the detergent. Transferring crystals to cryoconditions required a very careful protocol. Orthorhombic crystals diffract to 2.5 Å and tetragonal crystals to 2.2 Å.
doi:10.1107/S1744309105036262
PMCID: PMC1978154  PMID: 16511233
family 43 glycosidase hydrolases; xylosidases; hemicellulases; Geobacillus stearothermophilus; xylan; xylose
13.  An ortho­rhom­bic polymorph of pyrazino­[2,3-f][1,10]phenanthroline-2,3-dicarbonitrile 
The title compound, C16H6N6, is a polymorph of the previously reported structure [Kozlov & Goldberg (2008 ▶). Acta Cryst. C64, o498–o501]. Unlike the previously reported monoclinic polymorph (space group P21/c, Z = 8), the title compound reveals ortho­rhom­bic symmetry (space group Pnma, Z = 4). The mol­ecule shows crystallographic mirror symmetry, while the previously reported structure exhibits two independent mol­ecules per asymmetric unit. In the title compound, adjacent mol­ecules are essentially parallel along the c axis and tend to be vertical along the b axis with dihedral angles of 72.02 (6)°. However, in the reported polymorph, the entire crystal structure shows an anti­parallel arrangement of adjacent columns related by inversion centers and the two independent mol­ecules are nearly parallel with a dihedral angle of 2.48 (6)°.
doi:10.1107/S1600536811047039
PMCID: PMC3238907  PMID: 22199760
14.  A novel monoclinic phase of impurity-doped CaGa2S4 as a phosphor with high emission intensity 
In the solid-state synthesis of impurity-doped CaGa2S4, calcium tetra­thio­digallate(III), a novel phosphor material (denominated as the X-phase), with monoclinic symmetry in the space group P21/a, has been discovered. Its emission intensity is higher than that of the known ortho­rhom­bic polymorph of CaGa2S4 crystallizing in the space group Fddd. The asymmetric unit of the monoclinic phase consists of two Ca, four Ga and eight S sites. Each of the Ca and Ga atoms is surrounded by seven and four sulfide ions, respectively, thereby sharing each of the sulfur sites with the nearest neighbours. In contrast, the corresponding sites in the ortho­rhom­bic phase are surrounded by eight and four S atoms, respectively. The photoluminescence peaks from Mn2+ and Ce3+ in the doped X-phase, both of which are supposed to replace Ca2+ ions, have been observed to shift towards the high energy side in comparison with those in the ortho­rhom­bic phase. This suggests that the crystal field around the Mn2+ and Ce3+ ions in the X-phase is weaker than that in the ortho­rhom­bic phase.
doi:10.1107/S1600536812019113
PMCID: PMC3379052  PMID: 22719273
15.  Bis(1,10-phenanthroline-κ2 N,N′)(sulfato-O)copper(II) propane-1,3-diol monosolvate 
In the title compound, [Cu(SO4)(C12H8N2)2]·C3H8O2, the CuII ion is bonded to two chelating 1,10-phenanthroline (phen) ligands and one O atom from a monodentate sulfate ligand in a distorted square-based pyramidal arrangement, with the O atom in a basal site. The two chelating N2C2 groups subtend a dihedral angle of 71.10 (15)°. In the crystal, the solvent mol­ecule forms two O—H⋯O hydrogen bonds to its adjacent complex mol­ecule. The chosen crystal was found to be a racemic twin; the presence of pseudosymmetry in the structure suggests the higher symmetry space group C2/c, but attempts to refine the structure in this space group resulted in an unsatisfactory model and high R and wR values.
doi:10.1107/S1600536812047721
PMCID: PMC3588794  PMID: 23468759
16.  HisB from Mycobacterium tuberculosis: cloning, overexpression in Mycobacterium smegmatis, purification, crystallization and preliminary X-ray crystallographic analysis 
HisB from M. tuberculosis was cloned, overexpressed in M. smegmatis, purified and crystallized in three crystal forms.
HisB, encoded by open reading frame Rv1601, possesses enzymatic activity as an imidazoleglycerol-phosphate dehydratase in the histidine-biosynthetic pathway of Mycobacterium tuberculosis. A recombinant form of HisB was crystallized in three crystal forms: crystals grown using 20% PEG 1500 as a precipitant belonged to either the cubic space group P432 or the tetragonal space group P4, while an orthorhombic crystal form belonging to space group P21212 was obtained using 15% PEG 5000 and 10 mM MnCl2 as precipitant. The structure of HisB in the orthorhombic crystal form was solved by the molecular-replacement method using the crystal structure of its Arabidopsis thaliana counterpart, which shares 47% sequence identity with Rv1601, as the search model.
doi:10.1107/S1744309111037201
PMCID: PMC3212474  PMID: 22102255
HisB; Rv1601; Mycobacterium tuberculosis
17.  Crystallization and preliminary X-ray diffraction studies of AsaP1_E294A and AsaP1_E294Q, two inactive mutants of the toxic zinc metallopeptidase AsaP1 from Aeromonas salmonicida subsp. achromogenes  
Crystallization and preliminary X-ray diffraction studies of AsaP1_E294A and AsaP1_E294Q, two inactive mutants of the toxic zinc metallopeptidase AsaP1 from A. salmonicida subsp. achromogenes, are reported.
Two mutants of the toxic extracellular zinc endopeptidase AsaP1 (AsaP1_E294Q and AsaP1_E294A) of Aeromonas salmonicida subsp. achromogenes were expressed in Escherichia coli and crystallized by the vapour-diffusion method. Crystals were obtained using several precipitants and different protein concentrations. Protein crystals were found in a monoclinic (C2) as well as an orthorhombic (P212121) space group. The crystals belonging to the monoclinic space group C2 had unit-cell parameters a = 103.4, b = 70.9, c = 54.9 Å, β = 109.3° for AsaP1_E294A, and a = 98.5, b = 74.5, c = 54.7 Å, β = 112.4° for AsaP1_E294Q. The unit-cell parameters of the orthorhombic crystal obtained for AsaP1_E294A were a = 57.9, b = 60.2, c = 183.6 Å. The crystals of the two different mutants diffracted X-rays beyond 2.0 Å resolution.
doi:10.1107/S1744309109020132
PMCID: PMC2705637  PMID: 19574642
zinc metallopeptidases; Aeromonas salmonicida subsp. achromogenes
18.  Cloning, preparation and preliminary crystallographic studies of penicillin V acylase autoproteolytic processing mutants 
The production, crystallization and characterization of three inactive mutants of penicillin V acylase from B. sphaericus in their respective precursor and processed forms are reported. The space groups are different for the native enzyme and the mutants.
The crystallization of three catalytically inactive mutants of penicillin V acylase (PVA) from Bacillus sphaericus in precursor and processed forms is reported. The mutant proteins crystallize in different primitive monoclinic space groups that are distinct from the crystal forms for the native enzyme. Directed mutants and clone constructs were designed to study the post-translational autoproteolytic processing of PVA. The catalytically inactive mutants will provide three-dimensional structures of precursor PVA forms, plus open a route to the study of enzyme–substrate complexes for this industrially important enzyme.
doi:10.1107/S1744309104031227
PMCID: PMC1952408  PMID: 16508111
autoproteolysis; Ntn hydrolases; oxyanion holes; post-translational processing; precursor proteins; pro-peptides
19.  Bis(1,10-phenanthroline-κ2 N,N′)(sulfato-O)copper(II) ethane-1,2-diol monosolvate 
In the title compound, [Cu(SO4)(C12H8N2)2]·C2H6O2, the CuII ion is five-coordinated in a distorted square-pyramidal manner by four N atoms from two chelating 1,10-phenanthroline (phen) ligands and one O atom from a monodentate sulfate anion. The four N atoms comprise a square and the one O atom the apex of a square pyramid. The two chelating N2C2 groups are oriented at 71.1 (2)°. In the crystal, the components are connected by inter­molecular O—H⋯O hydrogen bonding. The presence of pseudosymmetry in the structure suggests the higher symmetry space group C2/c, but attempts to refine the structure in this space group resulted in an unsatisfactory model.
doi:10.1107/S1600536811031175
PMCID: PMC3200916  PMID: 22064689
20.  Monoclinic crystal form of Aspergillus niger α-­amylase in complex with maltose at 1.8 Å resolution 
Two new crystal structures of A. niger α-amylase are reported, one of which reveals two hitherto unobserved maltose-binding sites.
Aspergillus niger α-amylase catalyses the hydrolysis of α-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P212121 with one molecule per asymmetric unit and one belongs to the monoclinic space group P21 with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger α-amylase crystallized in the monoclinic space group P21 with two molecules per asymmetric unit in complex with maltose at 1.8 Å resolution is reported. Furthermore, a novel 1.6 Å resolution orthorhombic crystal form (space group P21212) of the native enzyme is presented. Four maltose molecules are observed in the maltose–α-amylase complex. Three of these occupy active-site subsites −2 and −1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products.
doi:10.1107/S1744309106024729
PMCID: PMC2242925  PMID: 16880540
α-amylase; Aspergillus niger; maltose; Aspergillus oryzae; TAKA-amylase
21.  N′-[(E)-4-Bromo­benzyl­idene]-2-(4-isobutyl­phen­yl)propanohydrazide 
The asymmetric unit of the title compound, C20H23BrN2O, contains two independent mol­ecules (A and B), in which the orientations of the 4-isobutyl­phenyl units are different. The dihedral angle between the two benzene rings is 88.45 (8)° in mol­ecule A and 89.87 (8)° in mol­ecule B. Mol­ecules A and B are linked by a C—H⋯N hydrogen bond. In the crystal, mol­ecules are linked into chains running along the a axis by inter­molcular N—H⋯O and C—H⋯O hydrogen bonds. The crystal structure is further stabilized by C—H⋯π inter­actions. The presence of pseudosymmetry in the structure suggests the higher symmetry space group Pbca. However, attempts to refine the structure in this space group resulted in a disorder model with high R (0.097) and wR (0.257) values. The crystal studied was an inversion twin with a 0.595 (4):0.405 (4) domain ratio.
doi:10.1107/S1600536809015542
PMCID: PMC2969560  PMID: 21583058
22.  Crystallographic characterization of two novel crystal forms of human insulin induced by chaotropic agents and a shift in pH 
Background
Insulin is a therapeutic protein that is widely used for the treatment of diabetes. Its biological function was discovered more than 80 years ago and it has since then been characterized extensively. Crystallization of the insulin molecule has always been a key activity since the protein is often administered by subcutaneous injections of crystalline insulin formulations. Over the years, insulin has been crystallized and characterized in a number of crystal systems.
Results
Interestingly, we have now discovered two new crystal forms of human insulin. The crystals were obtained when the two chaotropic agents, urea and thiocyanate were present in the crystallization experiments, and their structures were determined by X-ray crystallography. The crystals belong to the orthorhombic and monoclinic crystal systems, with space groups C2221 and C2 respectively. The orthorhombic crystals were obtained at pH 6.5 and contained three insulin hexamers in R6 conformation in the asymmetric unit whilst the monoclinic C2 crystals were obtained at pH 7.0 and contained one R6 hexamer in the asymmetric unit. Common for the two new crystals is a hexamer-hexamer interaction that has not been found in any of the previous crystal forms of insulin. The contacts involve a tight glutamate-glutamate interaction with a distance of 2.3 Å between groups. The short distance suggests a low barrier hydrogen bond. In addition, two tyrosine-tyrosine interactions occupying a known phenol binding pocket contribute to the stabilization of the contacts. Within the crystals, distinct binding sites for urea were found, adding further to the discussion on the role of urea in protein denaturation.
Conclusion
The change in space group from C2221 to C2 was primarily caused by an increase in pH. The fewer number of hexamer-hexamer interactions comprising the short hydrogen bond in the C2 space group suggest that pH is the driving force. In addition, the distance between the two glutamates increases from 2.32 Å in the C2221 crystals to 2.4 Å in the C2 crystals. However, in both cases the low barrier hydrogen bond and the tyrosine-tyrosine interaction should contribute to the stability of the crystals which is crucial when used in pharmaceutical formulations.
doi:10.1186/1472-6807-7-83
PMCID: PMC2241603  PMID: 18093308
23.  Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form 
The structure of the catalytic subunit of M. jannaschii aspartate transcarbamoylase has been determined in space group P212121 using synchrotron data to a resolution of 3.0 Å and was refined to a final R work and R free of 0.215 and 0.269, respectively.
Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallo­graphically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4° between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4° between crystal forms.
doi:10.1107/S1744309108025359
PMCID: PMC2531265  PMID: 18765902
aspartate transcarbamoylase; catalytic subunit; Methanococcus jannaschii
24.  Crystallization and preliminary crystallographic study of a recombinant predicted acetamidase/formamidase from the thermophile Thermoanaerobacter tengcongensis  
A predicated acetamidase/formanidase from the archaeon T. tengcongensis and its SeMet substitute have been crystallized and undergone preliminarily crystallographic studies including MAD data collection.
No crystal structures are yet available for homologues of a predicted acetamidase/formamidase (Amds/Fmds) from the archaeon Thermoanaerobacter tengcongensis. The Amds/Fmds gene was cloned and expressed as a soluble protein in Escherichia coli. Native Amds/Fmds and its SeMet-substituted form were purified and crystallized by vapour diffusion in hanging drops at 296 K. The native crystals, which were grown in PEG 8000, belong to the monoclinic space group P21, with unit-cell parameters a = 41.23 (3), b = 152.88 (6), c = 100.26 (7) Å, β = 99.49 (3)°. The diffraction data were collected to 2.00 Å resolution using synchrotron radiation. Based on a predicted solvent content of 50%, a Matthews coefficient of 2.44 Å3 Da−1 and two main peaks in the self-rotation function, the asymmetric unit is predicted to contain two dimers of the 32 kDa native protein. MAD data were collected for the SeMet protein, but the corresponding crystals display different unit-cell parameters and appear to contain four dimers in the asymmetric unit.
doi:10.1107/S1744309104030519
PMCID: PMC1952406  PMID: 16508105
acetamidase/formamidase; Thermoanaerobacter tengcongensis
25.  Crystallization and preliminary X-ray crystallographic studies of a new class of enoyl-(acyl-carrier protein) reductase, FabV, from Vibrio fischeri  
An orthorhombic crystal of an enoyl-(acyl-carrier protein) reductase from V. fischeri was obtained and diffraction data were collected to 2.7 Å resolution.
Enoyl-(acyl-carrier protein) reductase (ENR) catalyzes the last step of the fatty-acid elongation cycle of the bacterial fatty-acid biosynthesis (FAS II) pathway. Recently, a new class of ENR has been identified from Vibrio cholerae and was named FabV. In order to understand the molecular mechanism of the new class of ENR at the structural level, FabV from V. fischeri was overexpressed, purified and crystallized. Diffraction data were collected to 2.7 Å resolution from a native crystal. The crystal belonged to the orthorhombic space group P21212, with unit-cell parameters a = 123.53, b = 164.14, c = 97.07 Å. The presence of four molecules of FabV in the asymmetric unit gave a V M value of 2.81 Å3 Da−1, with a corresponding solvent content of 54.5%.
doi:10.1107/S1744309111049426
PMCID: PMC3253841  PMID: 22232178
FAS II pathway; enoyl-(acyl-carrier protein) reductase; Vibrio fischeri; FabV

Results 1-25 (732263)