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1.  Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRζ fragments 
P212121 crystals of SIV Nef core domain bound to a peptide fragment of the T-cell receptor ζ subunit exhibited noncrystallographic symmetry and nearly perfect pseudo-merohedral twinning simulating tetragonal symmetry. For a different peptide fragment, nontwinned tetragonal crystals were observed but diffracted to lower resolution. The structure was determined after assignment of the top molecular-replacement solutions to various twin or NCS domains followed by refinement under the appropriate twin law.
HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling ζ subunit of the T-­cell receptor (TCRζ). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCRζ fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCRζ polypeptide (Leu51–Asp93) was determined to 3.7 Å resolution (R work = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCRζ polypeptide (Ala63–Arg80) was determined to 2.05 Å resolution (R work = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P212121. The reduction in crystal space-group symmetry induced by the truncated TCRζ polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, −l) and a and b unit-cell parameters that were nearly identical predisposed the P212121 crystal form to pseudo-merohedral twinning.
doi:10.1107/S090744490904880X
PMCID: PMC2815668  PMID: 20124696
pseudo-merohedral twinning; noncrystallographic symmetry; pseudosymmetry; human immunodeficiency virus; Nef; T-cell receptor
2.  Three crystal forms of the bifunctional enzyme proline utilization A (PutA) from Bradyrhizobium japonicum  
The first diffraction-quality crystals of a PutA protein are reported. One of the three crystal forms described here exhibits pseudo-merohedral twinning. Removal of the N-terminal histidine tag aided the crystallization of another form.
Proline utilization A proteins (PutAs) are large (1000–1300 residues) membrane-associated bifunctional flavoenzymes that catalyze the two-step oxidation of proline to glutamate by the sequential action of proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase domains. Here, the first successful crystallization efforts for a PutA protein are described. Three crystal forms of PutA from Bradyrhizobium japonicum are reported: apparent tetragonal, hexagonal and centered monoclinic. The apparent tetragonal and hexagonal crystals were grown in the presence of PEG 3350 and sodium formate near pH 7. The apparent tetragonal form diffracted to 2.7 Å resolution and exhibited pseudo-merohedral twinning such that the true space group is P212121 with four molecules in the asymmetric unit. The hexagonal form diffracted to 2.3 Å resolution and belonged to space group P6222 with one molecule in the asymmetric unit. Centered monoclinic crystals were grown in ammonium sulfate, diffracted to 2.3 Å resolution and had two molecules in the asymmetric unit. Removing the histidine tag was important in order to obtain the C2 crystal form.
doi:10.1107/S174430910802842X
PMCID: PMC2564878  PMID: 18931443
proline utilization A; PutA; proline catabolism; proline dehydrogenase; P5C dehydrogenase; pseudo-merohedral twinning
3.  Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis  
Acta Crystallographica Section F  2012;68(Pt 9):1089-1093.
M. tuberculosis succinyl-diaminopimelate desuccinylase, the enzyme which catalyzes the seventh step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis indicated the presence of pseudo-merohedral twinning in space group P21, resulting in possible emulation of space group C2221.
Succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis (DapE, Rv1202) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Diffraction-quality crystals were obtained at acidic pH from ammonium sulfate and PEG and diffraction data were collected from two crystals to resolutions of 2.40 and 2.58 Å, respectively. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 Å, β = 119°. The most probable content of the asymmetric unit was two molecules of DapE, which would correspond to a solvent content of 56%. Both examined crystals turned out to be pseudo-merohedrally twinned, with twin operator −h, −k, h + l and twin fractions of approximately 0.46 and 0.16, respectively.
doi:10.1107/S174430911203062X
PMCID: PMC3433205  PMID: 22949202
succinyl-diaminopimelate desuccinylase; DapE; Rv1202; Mycobacterium tuberculosis
4.  Expression, purification, crystallization and structure determination of two glutathione S-transferase-like proteins from Shewanella oneidensis  
The production and purification of recombinant SoGST3 and SoGST6, two GST-like proteins from S. oneidensis, are reported and preliminary crystallographic studies of crystals of the recombinant enzymes are presented.
Genome analysis of Shewanella oneidensis, a Gram-negative bacterium with an unusual repertoire of respiratory and redox capabilities, revealed the presence of six glutathione S-transferase-like genes (sogst1–sogst6). Glutathione S-­transferases (GSTs; EC 2.5.1.18) are found in all kingdoms of life and are involved in phase II detoxification processes by catalyzing the nucleophilic attack of reduced glutathione on diverse electrophilic substrates, thereby decreasing their reactivity. Structure–function studies of prokaryotic GST-like proteins are surprisingly underrepresented in the scientific literature when compared with eukaryotic GSTs. Here, the production and purification of recombinant SoGST3 (SO_1576) and SoGST6 (SO_4697), two of the six GST-like proteins in S. oneidensis, are reported and preliminary crystallographic studies of crystals of the recombinant enzymes are presented. SoGST3 was crystallized in two different crystal forms in the presence of GSH and DTT that diffracted to high resolution: a primitive trigonal form in space group P31 that exhibited merohedral twinning with a high twin fraction and a primitive monoclinic form in space group P21. SoGST6 yielded primitive orthorhombic crystals in space group P212121 from which diffraction data could be collected to medium resolution after application of cryo-annealing protocols. Crystal structures of both SoGST3 and SoGST6 have been determined based on marginal search models by maximum-likelihood molecular replacement as implemented in the program Phaser.
doi:10.1107/S1744309108014589
PMCID: PMC2496851  PMID: 18540073
glutathione S-transferases; Shewanella oneidensis
5.  Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris  
The crystallization and preliminary X-ray diffraction analysis of sarcosine dimethylglycine methyltransferase from H. halochoris is reported.
Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-­adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution.
doi:10.1107/S1744309109026232
PMCID: PMC2720339  PMID: 19652345
sarcosine dimethylglycine methyltransferase; Halorhodospira halochoris; twinning
6.  Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase 
X-ray crystallographic analysis of human inosine triphosphate pyrophosphohydrolase provided the secondary structure and active-site structure at 1.6 Å resolution in an orthorhombic crystal form. The structure gives a framework for future structure–function studies employing site-directed mutagenesis and for the identification of substrate/product-binding sites.
The structure of human inosine triphosphate pyrophosphohydrolase (ITPA) has been determined using diffraction data to 1.6 Å resolution. ITPA contributes to the accurate replication of DNA by cleansing cellular dNTP pools of mutagenic nucleotide purine analogs such as dITP or dXTP. A similar high-resolution unpublished structure has been deposited in the Protein Data Bank from a monoclinic and pseudo-merohedrally twinned crystal. Here, cocrystallization of ITPA with a molar ratio of XTP appears to have improved the crystals by eliminating twinning and resulted in an orthorhombic space group. However, there was no evidence for bound XTP in the structure. Comparison with substrate-bound NTPase from a thermophilic organism predicts the movement of residues within helix α1, the loop before α6 and helix α7 to cap off the active site when substrate is bound.
doi:10.1107/S1744309106041790
PMCID: PMC2225220  PMID: 17077483
inosine triphosphate pyrophosphohydrolase
7.  Towards structural studies of the old yellow enzyme homologue SYE4 from Shewanella oneidensis and its complexes at atomic resolution 
Of the four old yellow enzyme homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method.
Shewanella oneidensis is an environmentally versatile Gram-negative γ-proteo­bacterium that is endowed with an unusually large proteome of redox proteins. Of the four old yellow enzyme (OYE) homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the ortho­rhombic space group P212121 and were moderately pseudo-merohedrally twinned, emulating a P422 metric symmetry. The native crystals of SYE4 were of exceptional diffraction quality and provided complete data to 1.10 Å resolution using synchrotron radiation, while crystals of the reduced enzyme and of the enzyme in complex with a wide range of ligands typically led to high-quality complete data sets to 1.30–1.60 Å resolution, thus providing a rare opportunity to dissect the structure–function relationships of a good-sized enzyme (40 kDa) at true atomic resolution. Here, the attainment of a number of experimental milestones in the crystallographic studies of SYE4 and its complexes are reported, including isolation of the elusive hydride–Meisenheimer complex.
doi:10.1107/S1744309109050386
PMCID: PMC2805545  PMID: 20057079
SYE4; Shewanella oneidensis; old yellow enzyme homologues
8.  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.
doi:10.1107/S0907444909039912
PMCID: PMC2789005  PMID: 19966420
pseudosymmetry; structure determination; cysteine proteases; Mac-1
9.  Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2′′-phosphotransferase-IVa 
Aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] is an enzyme that is responsible for high-level gentamicin resistance in E. casseliflavus isolates. Three different crystals of wild-type substrate-free APH(2′′)-IVa have been prepared and preliminary X-ray diffraction experiments have been undertaken on all three crystal forms.
The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, although one of the crystal forms had a unit-cell volume that was approximately 13% smaller than the other and a very low solvent content of around 38%. The third crystal form belonged to the monoclinic space group P21 and preliminary X-ray diffraction analysis was consistent with the presence of two molecules in the asymmetric unit. The orthorhombic crystal forms of apo APH(2′′)-IVa both diffracted to 2.2 Å resolution and the monoclinic crystal form diffracted to 2.4 Å resolution; synchrotron diffraction data were collected from these crystals at SSRL (Stanford, California, USA). Structure determination by molecular replacement using the structure of the related enzyme APH(2′′)-IIa is proceeding.
doi:10.1107/S1744309109050039
PMCID: PMC2805544  PMID: 20057078
aminoglycoside-2′′-phosphotransferase-IVa; Enterococcus casseliflavus; antibiotic resistance
10.  Dichloridobis(pyridine-2-thiol­ato-κ2 N,S)tin(IV): a new polymorph 
The title compound, [SnCl2(C5H4NS)2], is the product of reaction of 2,2′-dipyridyl disulfide with tin tetra­chloride. The SnIV atom adopts a distorted octa­hedral geometry, with the two bidentate pyridine-2-thiol­ate ligands forming two planar four-membered chelate rings. The two Sn—Cl, two Sn—N and two Sn—S bonds are in cis, cis and trans configurations, respectively. The crystal grown from acetonitrile represents a new monoclinic polymorph in space group C2/c with the mol­ecule having twofold rotational symmetry, the SnIV atom lying on the twofold axis. The mol­ecular structure of the monoclinic polymorph is very close to that of the triclinic polymorph studied previously in space group P-1, the mol­ecule occupying a general position [Masaki & Matsunami (1976 ▶). Bull. Chem. Soc. Jpn, 49, 3274–3279; Masaki et al. (1978 ▶). Bull. Chem. Soc. Jpn, 51, 3298–3301]. Apparently, the formation of the two polymorphs is determined by the different systems of inter­molecular inter­actions. In the crystal of the monoclinic polymorph, mol­ecules are bound into ribbons along the c axis by C—H⋯Cl hydrogen bonds, whereas in the crystal of the triclinic polymorph, mol­ecules form chains along the a axis by attractive S⋯S inter­actions. The crystal studied was a pseudo-merohedral twin; the refined BASF value is 0.221 (1).
doi:10.1107/S1600536812024026
PMCID: PMC3393155  PMID: 22807723
11.  5-[(1R,2R,4R)-2-Meth­oxy-1,7,7-tri­methylbi­cyclo­[2.2.1]hept-2-yl]-1H-tetra­zole 
The title compound, C12H20N4O, undergoes a phase transition on cooling. The room-temperature structure is tetra­gonal (P43212, Z′ = 1), with the meth­oxy­bornyl group being extremely disordered. Below 213 K the structure is ortho­rhom­bic (P212121, Z′ = 2), with ordered mol­ecules. The two independent mol­ecules (A and B) have very similar conformations; significant differences only occur for the torsion angles about the Cborn­yl—Ctetra­zole bonds. The independent mol­ecules are approximately related by the pseudo-symmetry relation: xB = −1/4 + yA, yB = 3/4 - xA and zB = 1/4 + zA. In the crystal, mol­ecules are connected by N—H⋯N hydrogen bonds between the tetra­zole groups, forming a pseudo-43 helix parallel to the c-axis direction. The crystal studied was a merohedral twin with a refined twin fraction value of 0.231 (2).
doi:10.1107/S1600536813014700
PMCID: PMC3772465  PMID: 24046608
12.  Improvement of crystal quality by surface mutations of β-lactamase Toho-1 
By introducing surface mutations, the crystal quality of a β-lactamase, Toho-1, was drastically improved. The resultant crystals showed no tendency towards merohedral twinning and diffracted to 0.97 Å resolution.
The β-lactamase Toho-1 exhibits a strong tendency to form merohedrally twinned crystals. Here, the crystal quality of Toho-1 was improved by using surface modification to remove a sulfate ion involved in crystal packing. The surface-modified Toho-1 variant (R274N/R276N) was crystallized under similar conditions to those used for wild-type Toho-1. R274N/R276N did not form merohedrally twinned crystals. The crystals diffracted to a significantly higher resolution (∼0.97 Å) than the wild-type crystals (1.65 Å); they belonged to the same space group and had almost identical unit-cell parameters to those of wild-type Toho-­1.
doi:10.1107/S1744309109008240
PMCID: PMC2664765  PMID: 19342785
extended-spectrum β-lactamases; crystal contacts; surface mutations; ultra-high resolution; merohedral twinning
13.  Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya  
The Kunitz-type trypsin/chymotrypsin inhibitor isolated from C. papaya latex has been crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms are observed, diffracting to 2.6 and 1.7 Å.
A Kunitz-type protease inhibitor purified from the latex of green papaya (Carica papaya) fruits was crystallized in the presence and absence of divalent metal ions. Crystal form I, which is devoid of divalent cations, diffracts to a resolution of 2.6 Å and belongs to space group P31 or P32. This crystal form is a merohedral twin with two molecules in the asymmetric unit and unit-cell parameters a = b = 74.70, c = 78.97 Å. Crystal form II, which was grown in the presence of Co2+, diffracts to a resolution of 1.7 Å and belongs to space group P212121, with unit-cell parameters a = 44.26, b = 81.99, c = 140.89 Å.
doi:10.1107/S1744309106046367
PMCID: PMC2225369  PMID: 17142906
protease inhibitors; detwinning
14.  Expression, purification and crystallization of the ecto-enzymatic domain of rat E-NTPDase1 CD39 
The ecto-enzymatic domain of rat E-NTPDase1 CD39 was expressed and purified and diffraction-quality crystals of the enzyme were obtained.
CD39 is a prototype member of the ecto-nucleoside triphosphate diphospho­hydrolase family that hydrolyzes extracellular nucleoside diphosphates and triphosphates in the presence of divalent cations. Here, the expression, purification and crystallization of the ecto-enzymatic domain of rat CD39, sCD39, are described. The 67 kDa secreted soluble glycoprotein was recombinantly overexpressed in a glycosylation mutant CHO line, Lec.3.2.8.1, and purified from conditioned media. Diffraction-quality crystals of sCD39 were produced by the vapor-diffusion method using PEG 3350 and ammonium dihydrogen phosphate as precipitants. The enzyme crystallized in a primitive trigonal form in space group P32, with unit-cell parameters a = b = 118.1, c = 81.6 Å and with two sCD39 copies in the asymmetric unit. Several low- to medium-resolution diffraction data sets were collected using an in-house X-ray source. Analysis of the intensity statistics showed that the crystals were invariably merohedrally twinned with a high twin fraction. For initial phasing, a molecular-replacement search was performed against the complete 3.2 Å data set using a maximum-likelihood molecular-replacement method as implemented in Phaser. The initial model of the two sCD39 monomers was placed into the P32 lattice and rigid-body refined and position-minimized with PHENIX.
doi:10.1107/S1744309108032569
PMCID: PMC2581708  PMID: 18997343
CD39; ecto-nucleoside triphosphate diphosphohydrolases
15.  Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design 
Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects.
RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P41212 or P43212. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported.
doi:10.1107/S1744309105035888
PMCID: PMC1978144  PMID: 16511232
adenosine deaminase acting on RNA; twinning; RNA; bulged loop; internal loop
16.  Two polymorphs of chlorido(cyclo­hexyl­diphenyl­phosphine)gold(I) 
The title compound, [AuCl(C18H21P)], a monomeric two-coordinate gold(I) complex, has been characterized at 100 K as two distinct monoclinic polymorphs, one from a single crystal, (Is), and one from a pseudo-merohedrally twinned crystal, (It). The mol­ecular structures in the two monoclinic [P21/n for (Is) and P21/c for (It)] polymorphs are similar; however, the packing arrangements in the two lattices differ considerably. The structure of (It) is pseudo-merohedrally twinned by a twofold rotation about the a* axis.
doi:10.1107/S0108270110001861
PMCID: PMC2855583  PMID: 20203394
17.  Expression, purification and crystallization of class C acid phosphatases from Francisella tularensis and Pasteurella multocida  
Two members of the class C family of bacterial nonspecific acid phosphatases have been cloned, expressed, purified and crystallized. One of the crystal forms exhibited epitaxial twinning.
Class C nonspecific acid phosphatases are bacterial enzymes that are secreted across the cytoplasmic membrane and hydrolyze a variety of phosphomono­esters at acidic pH. These enzymes are of interest for the development of improved vaccines and clinical diagnostic methods. In one case, the category A pathogen Francisella tularensis, the class C phosphatase plays a role in bacterial fitness. Here, the cloning, expression, purification and crystallization methods for the class C acid phosphatases from F. tularensis and Pasteurella multocida are reported. Crystals of the F. tularensis enzyme diffracted to 2.0 Å resolution and belonged to space group C2221, with one enzyme molecule in the asymmetric unit. Crystals of the P. multocida enzyme diffracted to 1.85 Å resolution and belonged to space group C2, with three molecules in the asymmetric unit. Diffraction patterns from crystals of the P. multocida enzyme exhibited multiple interpenetrating reciprocal-space lattices, indicating epitaxial twinning. Despite this aberrance, autoindexing was robust and the data could be satisfactorily processed to 1.85 Å resolution using MOSFLM and SCALA.
doi:10.1107/S1744309109001511
PMCID: PMC2650447  PMID: 19255471
acid phosphatases; class C nonspecific acid phosphatases; Francisella tularensis; Pasteurella multocida; epitaxial twinning
18.  Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 Å resolution 
The crystal structure of the H107R variant of the extracellular domain of mouse NKR-P1A was determined using X-ray diffraction from a merohedrally twinned crystal.
The structure of the H107R variant of the extracellular domain of the mouse natural killer cell receptor NKR-P1A has been determined by X-ray diffraction at 2.3 Å resolution from a merohedrally twinned crystal. Unlike the structure of the wild-type receptor in space group I4122 with a single chain per asymmetric unit, the crystals of the variant belonged to space group I41 with a dimer in the asymmetric unit. Different degrees of merohedral twinning were detected in five data sets collected from different crystals. The mutation does not have a significant impact on the overall structure, but led to the binding of an additional phosphate ion at the interface of the molecules.
doi:10.1107/S1744309111046203
PMCID: PMC3232129  PMID: 22139156
NKR-P1A; merohedral twinning; mutation
19.  Crystallization and preliminary X-ray diffraction studies of a ferredoxin reductase component of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1 
The ferredoxin reductase component of carbazole 1,9a-dioxygenase (Red) is involved in electron transfer from NAD(P)H to ferredoxin. The class IIA Red from Novosphingobium sp. KA1 was crystallized and the crystal diffracted to a resolution of 1.58 Å.
Carbazole 1,9a-dioxygenase (CARDO) is the initial enzyme of the carbazole-degradation pathway. The CARDO of Novosphingobium sp. KA1 consists of a terminal oxygenase, a putidaredoxin-type ferredoxin and a ferredoxin-NADH oxidoreductase (Red) and is classified as a class IIA Rieske oxygenase. Red from KA1 was crystallized at 278 K by the hanging-drop vapour-diffusion method using PEG 4000. The crystal diffracted to 1.58 Å resolution and belonged to space group P32, with unit-cell parameters a = b = 92.2, c = 78.6 Å, α = γ = 90, β = 120°. Preliminary analysis of the X-ray diffraction data revealed that the asymmetric unit contained two Red monomers. The crystal appeared to be a merohedral twin, with a twin fraction of 0.32 and twin law (−h, −k, l).
doi:10.1107/S1744309110014491
PMCID: PMC2882777  PMID: 20516607
carbazole; Rieske nonhaem iron oxygenases; ferredoxin reductases
20.  X-ray diffraction studies on merohedrally twinned Δ1–62NtNBCe1-A crystals of the sodium/bicarbonate cotransporter 
A truncated mutant missing the first 62 residues of the N-terminal, cytoplasmic domain of the sodium-bicarbonate NBCe1-A cotransporter crystallizes in space group P31 with pseudo-P3121 symmetry and a hemihedral twin fraction of 33.0%. Twinned fractions and twin-pair statistics over binned resolutions confirm that the calculated twin fraction is associated with hemihedral twinning and not to non-crystallographic symmetry.
NBCe1-A membrane-embedded macromolecules that cotransport sodium and bicarbonate ions across the bilayer serve to maintain acid–base homeostasis throughout the body. Defects result in a number of renal and eye disorders, including type-II renal tubular acidosis and cataracts. Here, crystals of a human truncated mutant of the cytoplasmic N-terminal domain of NBCe1 (Δ1–62NtNBCe1-A) are reported that diffract X-rays to 2.4 Å resolution. The crystal symmetry of Δ1–62NtNBCe1-A is of space group P31 with pseudo-P3121 symmetry and it has a hemihedral twin fraction of 33.0%. The crystals may provide insight into the pathogenic processes observed in a subset of patients with truncating and point mutations in the gene encoding NBCe1.
doi:10.1107/S1744309113016710
PMCID: PMC3702328  PMID: 23832211
NBCe1; bicarbonate transport
21.  Preliminary X-ray analysis of cellobiohydrolase Cel7B from Melanocarpus albomyces  
The crystallization and preliminary X-ray diffraction analysis of cellobiohydrolase from M. albomyces is reported.
Cellobiohydrolases are enzymes that cleave off cellobiose units from cellulose chains in a processive manner. Melanocarpus albomyces Cel7B is a thermostable single-module cellobiohydrolase that has relatively low activity on small soluble substrates at room temperature. It belongs to glycoside hydrolase family 7, which includes endo-β-1,4-glucanases and cellobiohydrolases. Cel7B was crystallized using the hanging-drop vapour-diffusion method and streak-seeding. The crystals belonged to space group P21, with unit-cell parameters a = 50.9, b = 94.5, c = 189.8 Å, β = 90.0° and four monomers in the asymmetric unit. Analysis of the intensity statistics showed that the crystals were pseudo-merohedrally twinned, with a twinning fraction of 0.37. X-ray diffraction data were collected at 1.6 Å resolution using synchrotron radiation.
doi:10.1107/S1744309107034458
PMCID: PMC2376320  PMID: 17768346
cellulase; cellobiohydrolase; twinning
22.  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
23.  X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 Å resolution using a twinned crystal 
The crystal structure of bilirubin oxidase (BOD) from M. verrucaria has been determined at 2.3 Å resolution using a merohedrally twinned crystal. BOD has four copper-coordination sites that are almost identical to those of other multicopper oxidases and is also very similar to them in overall structure.
Bilirubin oxidase (BOD), a multicopper oxidase found in Myrothecium verrucaria, catalyzes the oxidation of bilirubin to biliverdin. Oxygen is the electron acceptor and is reduced to water. BOD is used for diagnostic analysis of bilirubin in serum and has attracted considerable attention as an enzymatic catalyst for the cathode of biofuel cells that work under neutral conditions. Here, the crystal structure of BOD is reported for the first time. Blue bipyramid-shaped crystals of BOD obtained in 2-methyl-2,4-pentanediol (MPD) and ammonium sulfate solution were merohedrally twinned in space group P63. Structure determination was achieved by the single anomalous diffraction (SAD) method using the anomalous diffraction of Cu atoms and synchrotron radiation and twin refinement was performed in the resolution range 33–2.3 Å. The overall organization of BOD is almost the same as that of other multicopper oxidases: the protein is folded into three domains and a total of four copper-binding sites are found in domains 1 and 3. Although the four copper-binding sites were almost identical to those of other multicopper oxidases, the hydrophilic Asn residue (at the same position as a hydrophobic residue such as Leu in other multicopper oxidases) very close to the type I copper might contribute to the characteristically high redox potential of BOD.
doi:10.1107/S1744309110018828
PMCID: PMC2898457  PMID: 20606269
bilirubin oxidase; twinned crystals; multicopper enzymes; Myrothecium verrucaria
24.  Crystallization and preliminary X-ray analysis of allene oxide synthase, cytochrome P450 CYP74A2, from Parthenium argentatum  
Allene oxide synthase, an atypical cytochrome P450 from Parthenium argentatum, was crystallized and diffraction data were collected to 2.4 Å resolution.
Oxylipins are oxygenated derivatives of fatty acids and pivotal signaling molecules in plants and animals. Allene oxide synthase (AOS) is a key cytochrome P450 CYP74 enzyme involved in the biosynthesis of plant oxylipin jasmonates to convert 13(S)-hydroperoxide to allene oxide. Guayule (Parthenium argentatum) AOS, CYP74A2, was expressed in Escherichia coli. Protein was purified using affinity chromatography and size exclusion chromatography, and then crystallized. Two different crystal forms were obtained from 0.2 M (NH4)H2PO4, 50% MPD, 0.1 M Tris, pH 8.5 at 277 K using the hanging-drop vapor-diffusion method. Preliminary X-ray analysis was carried out, and the crystals were found to belong to the tetragonal space group I422 with cell parameters a = b = 126.5, c = 163.9 Å, and the monoclinic space group C2 with cell parameters a = 336.5, b = 184.2, c = 159.0 Å, β = 118.6°. Diffraction data were collected to 2.4 Å resolution from a tetragonal form of crystal using a home X-ray source.
doi:10.1107/S1744309108017545
PMCID: PMC2443977  PMID: 18607105
allene oxide synthase; cytochrome P450 CYP74A2; oxylipin; jasmonate; guayule (Parthenium argentatum); crystallization
25.  Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulatory domain of aspartokinase (Rv3709c) from Mycobacterium tuberculosis  
The regulatory domain of M. tuberculosis aspartokinase, the enzyme which catalyses the first reaction step in the biosynthesis of the amino acids lysine, methionine and threonine, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis of several crystals revealed the presence of five distinct crystal forms.
The regulatory domain of Mycobacterium tuberculosis aspartokinase (Mtb-AK, Mtb-Ask, Rv3709c) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Screening for initial crystallization conditions using the regulatory domain (AK-β) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for X-ray diffraction analysis. From these four conditions five different crystal forms of Mtb-AK-β resulted, three of which belonged to the orthorhombic system, one to the tetragonal system and one to the monoclinic system. The highest resolution (1.6 Å) was observed for a crystal form belonging to space group P212121, with unit-cell parameters a = 53.70, b = 63.43, c = 108.85 Å and two molecules per asymmetric unit.
doi:10.1107/S1744309111000030
PMCID: PMC3053168  PMID: 21393848
aspartokinase; Rv3709c; Mycobacterium tuberculosis; tuberculosis

Results 1-25 (919236)