Biological Crystallography

 

Acta Cryst. (2002). D58, 1085-1091  [ doi:10.1107/S0907444902006261 ]

Ultrahigh-resolution structure of high-potential iron-sulfur protein from Thermochromatium tepidum

L. Liu, T. Nogi, M. Kobayashi, T. Nozawa and K. Miki

Synopsis: The crystal structure of the high-potential iron-sulfur protein from T. tepidum was refined using low-temperature diffraction data to 0.80  Å resolution collected using synchrotron radiation. The electron transfer is discussed based on the hydrophobic interaction and molecular packing.

PDB reference: 1iua

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1092-1098  [ doi:10.1107/S0907444902006510 ]

Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases

P. D. Sun, S. Radaev and M. Kattah

Synopsis: Using lysozyme and Fc receptor crystals as test cases, it was demonstrated that conventional heavy-atom derivatives could be generated by quick soaking in a 10  min to 2  h time frame instead of days. Derivatives generated in this way showed stronger heavy-atom signals and appeared to be more isomorphous to the native than derivatives generated by overnight soaks.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1099-1103  [ doi:10.1107/S0907444902006522 ]

Generating isomorphous heavy-atom derivatives by a quick-soak method. Part II: phasing of new structures

P. D. Sun and S. Radaev

Synopsis: A quick-soak method was used to generate heavy-atom derivatives for the de novo phasing of two structures. The derivatives generated this way were not only sufficient for phasing, but were also better diffracting and more isomorphous to the natives than derivatives soaked overnight.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1104-1110  [ doi:10.1107/S0907444902006534 ]

Structure of cytochrome c₆ from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell

C. A. Kerfeld, M. R. Sawaya, D. W. Krogmann and T. O. Yeates

Synopsis: An isoform of cytochrome c₆ from the cyanobacterium A. maxima crystallized in space group I4₁32, with eight molecules in the asymmetric unit. The crystal structure reveals protein molecules packed into hollow clusters of 24 molecules.

PDB reference: 1kib

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1111-1117  [ doi:10.1107/S0907444902006509 ]

Thiol-reactive lanthanide chelates for phasing protein X-ray diffraction data

M. D. Purdy, P. Ge, J. Chen, P. R. Selvin and M. C. Wiener

Synopsis: A thiol-reactive lanthanide chelate was used to incorporate ordered dysprosium ions into crystals of a 34  kDa test protein. Data collected from these crystals in-house and at a synchrotron beamline possessed a large anomalous signal, which enabled calculation of high-quality SAD phases in both cases.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1118-1128  [ doi:10.1107/S090744490200656X ]

The 1.35  Å structure of cadmium-substituted TM-3, a snake-venom metalloproteinase from Taiwan habu: elucidation of a TNF-converting enzyme-like active-site structure with a distorted octahedral geometry of cadmium

K.-F. Huang, S.-H. Chiou, T.-P. Ko, J.-M. Yuann and A.H.-J. Wang

Synopsis: The high-resolution crystal structure of a snake-venom metalloproteinase (SVMP), TM-3, was solved, which appears to have a stronger resemblance among the known structures of SVMP to the crystal structure of catalytic domain of TNF-converting enzyme (TACE).

PDB reference: 1kuf

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1129-1137  [ doi:10.1107/S0907444902006601 ]

An enzyme with a deep trefoil knot for the active-site architecture

O. Nureki, M. Shirouzu, K. Hashimoto, R. Ishitani, T. Terada, M. Tamakoshi, T. Oshima, M. Chijimatsu, K. Takio, D. G. Vassylyev, T. Shibata, Y. Inoue, S. Kuramitsu and S. Yokoyama

Synopsis: The crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from T. thermophilus (RrmA) has been determined at 2.4  Å resolution and a deep trefoil knot has been found for the first time.

PDB reference: 1ipa

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1138-1146  [ doi:10.1107/S0907444902006698 ]

NH₃-dependent NAD⁺ synthetase from Bacillus subtilis at 1  Å resolution

J. Symersky, Y. Devedjiev, K. Moore, C. Brouillette and L. DeLucas

Synopsis: An atomic resolution structure of the NAD⁺ synthetase is presented with implications for the catalytic mechanism.

PDB reference: 1kqp

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1147-1154  [ doi:10.1107/S0907444902006959 ]

Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling

J. A. Gavira, D. Toh, J. Lopéz-Jaramillo, J. M. García-Ruíz and J. D. Ng

Synopsis: The crystallization, cryoprotection and heavy-atom derivatization of insulin have been optimized using the counter-diffusion technique in a restricted geometry. The protein crystals obtained were immediately used for in situ X-ray diffraction, phase determination by SAS and electron-density map calculation without crystal manipulation.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1155-1161  [ doi:10.1107/S0907444902007138 ]

Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state

B. K. Biswal and M. Vijayan

Synopsis: The structure analysis of high-salt crystals of oxy- and deoxyhaemoglobin at different levels of environmental humidity and solvent content appears to indicate that the deoxy form can access an ensemble of related T states.

PDB references: 1lfq, 1lft, 1lfv, 1lfy, 1lfz and 1lfl

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1162-1167  [ doi:10.1107/S0907444902007126 ]

Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme

N. T. Saraswathi, R. Sankaranarayanan and M. Vijayan

Synopsis: A comparative study involving monoclinic lysozyme crystals grown in the presence of sucrose, trehalose, sorbitol and glycerol suggests that the stabilizing additives have no significant effect on the structure of the enzyme and the organization of the ordered water molecules around it.

PDB references: 1lj3, 1lj4, 1lje, 1ljf, 1ljg, 1ljh, 1lji, 1ljj and 1ljk

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1168-1174  [ doi:10.1107/S090744490200714X ]

Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3  Å resolution

K. Kawasaki, H. Kondo, M. Suzuki, S. Ohgiya and S. Tsuda

Synopsis: The crystal structure of B. subtilis lipase was determined at 1.3  Å resolution. A substrate-binding model is proposed on the basis of the presence of alternate conformations in the side chain of the catalytic serine residue and a glycerol molecule in the active site.

PDB reference: 1isp

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1175-1181  [ doi:10.1107/S0907444902007254 ]

Structure of the functional domain of the major grass-pollen allergen Phlp 5b

K. Rajashankar, A. Bufe, W. Weber, S. Eschenburg, B. Lindner and Ch. Betzel

Synopsis: As an important step in understanding the interactions between the pollen protein and components of the human immune system, the structure of the C-terminal key domain of the major allergen Phlp 5b from timothy grass pollen has been determined at 2.0  Å. It is the first known allergen composed entirely out of -helices.

PDB reference: 1l3p

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1182-1192  [ doi:10.1107/S0907444902007849 ]

Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase

P. A. Elkins, Y. S. Ho, W. W. Smith, C. A. Janson, K. J. D'Alessio, M. S. McQueney, M. D. Cummings and A. M. Romanic

Synopsis: The X-ray crystal structure of the proform of human matrix metalloproteinase MMP9 has been solved to 2.5  Å resolution. The design of MMP9 inhibitors may be able to exploit the shape of the S1' binding pocket for specificity.

PDB reference: 1l6j

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1193-1194  [ doi:10.1107/S0907444902005498 ]

Crystallization and preliminary X-ray crystallographic studies on recombinant human carnitine acetyltransferase

W. Lian, L. Govindasamy, Y. Gu, T. Kukar, M. Agbandje-McKenna, R. McKenna and D. Wu

Synopsis: Crystals of carnitine acetyltransferase are reported to diffract X-rays to 1.6  Å resolution. This enzyme catalyzes the transfer of short-chain acyl groups to CoA.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1195-1197  [ doi:10.1107/S0907444902007928 ]

Crystallization and preliminary X-ray crystallographic studies of HLA-A*1101 complexed with an HIV-1 decapeptide

L. Li, N. Promadej, J. M. McNicholl and M. Bouvier

Synopsis: The first soluble recombinant class I HLA-A*1101 molecule has been expressed and refolded in vitro with 2-microglobulin and a Nef decapeptide. The complex was crystallized and X-ray diffraction data to 2.2  Å resolution were collected.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1198-1200  [ doi:10.1107/S0907444902008417 ]

Crystallization of a stringent response factor from Aquifex aeolicus

O. Kristensen, M. Laurberg and M. Gajhede

Synopsis: Mutations and deliberate oxidation of the protein have been used to enhance the possibilities of experimental phasing. The variant protein crystallized under different conditions to the wild-type protein and produced a crystal form of increased physical stability.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1201-1203  [ doi:10.1107/S0907444902006583 ]

Purification and initial crystallization studies of a DnaB intein from Synechocystis sp. PCC 6803

X. Chen, M.-Q. Xu, Y. Ding, S. Ferrandon and Z. Rao

Synopsis: A 154-residue mini-intein from the dnaB gene of Synechocystis sp. PCC 6803 (Ssp DnaB intein) has been purified and crystallized using PEG 4000 as a precipitant.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1204-1206  [ doi:10.1107/S0907444902006571 ]

Crystallographic study of a naturally occurring trans-splicing intein from Synechocystis sp. PCC 6803

X. Chen, M.-Q. Xu, Y. Ding, S. Ferrandon and Z. Rao

Synopsis: A naturally occurring split intein from the dnaE gene of Synechocystis sp. PCC6803 (Ssp DnaE intein) has been purified and crystallized using PEG 8K as precipitant.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1207-1210  [ doi:10.1107/S0907444902006960 ]

Crystallization and preliminary X-ray analysis of the Escherichia coli adaptor protein ClpS, free and in complex with the N-terminal domain of ClpA

K. Zeth, D. A. Dougan, S. Cusack, B. Bukau and R. B. Ravelli

Synopsis: Crystallization and preliminary analysis of the substrate-sensor protein ClpS from E. coli alone and in complex with the N-terminal substrate-binding domain of ClpA is reported.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1211-1213  [ doi:10.1107/S090744490200700X ]

Expression, purification, crystallization and preliminary X-ray analysis of rat ecto-ADP-ribosyltransferase 2 (ART2.2)

C. Mueller-Dieckmann, T. Scheuermann, K. Wursthorn, J. Schröder, F. Haag, G. E. Schulz and F. Koch-Nolte

Synopsis: Rat ecto-ADP-ribosyltransferase (ART2.2) has been expressed in the periplasm of E. coli, purified and crystallized in three forms diffracting to high resolution.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1214-1216  [ doi:10.1107/S0907444902007357 ]

Crystallization and preliminary crystallographic studies of human TGF- type II receptor ligand-binding domain

C. C. Boesen, S. A. Motyka, A. Patamawenu and P. D. Sun

Synopsis: Various truncations of the extracellular domain of human TGF- receptor have been expressed for crystallizations. Among them, TBRII (27-136)yielded crystals diffracting to 1.05  Å resolution.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1217-1219  [ doi:10.1107/S0907444902007369 ]

Crystallization and preliminary X-ray crystallographic analysis of a yedU gene product from Escherichia coli

O.-G. Kim, I.-K. Kim, G.-H. Kim, J. Ko, C. Park, P.-G. Suh, S.-O. Kang, H.-S. Lee and S.-S. Cha

Synopsis: A yedU gene product with a molecular mass of 31  kDa is a hypothetical protein with no known function. The protein was purified and crystallized at 296  K.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1220-1223  [ doi:10.1107/S0907444902007345 ]

Crystallization of a nickel-containing superoxide dismutase and preliminary phase determination by MAD at the Ni K edge

J. Wuerges, J.-W. Lee, S.-O. Kang and K. Djinovic Carugo

Synopsis: Nickel-containing superoxide dismutase belongs to a new class of superoxide dismutases. It has been crystallized in various crystal forms and initial phase information has been obtained by MAD at the Ni K edge.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1224-1225  [ doi:10.1107/S0907444902007370 ]

Preliminary crystallographic analysis of the cysteine desulfurase IscS from Escherichia coli

H. D. Urbina, J. R. Cupp-Vickery and L. E. Vickery

Synopsis: Crystals of E. coli IscS were prepared, and a native X-ray diffraction data set was obtained to a resolution of 2.1  Å.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1226-1228  [ doi:10.1107/S0907444902007382 ]

Purification, crystallization and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis, the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway

A. B. Merkel, G. K. Temple, M. D. Burkart, H. C. Losey, K. Beis, C. T. Walsh and J. H. Naismith

Synopsis: Vancomycin is the last line of defence in the treatment of Gram-positive infection. It is a complex molecule composed of carbohydrate and cyclized peptides. The crystallization of dTDP-3-amino-4-keto 2,3,6-trideoxy-3-C-methyl-glucose-5-epimerase, an enzyme involved in the synthesis of the carbohydrate portion of the compound, is reported.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1229-1231  [ doi:10.1107/S090744490200762X ]

Crystallization and preliminary X-ray diffraction studies of the water-soluble state of the pore-forming toxin sticholysin II from the sea anemone Stichodactyla helianthus

J. M. Mancheño, M. Martínez-Ripoll, J. G. Gavilanes and J. A. Hermoso

Synopsis: The eukaryotic pore-forming toxin sticholysin II has been crystallized by the hanging-drop vapour-diffusion method. Native data have been collected to 1.71  Å resolution.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1232-1233  [ doi:10.1107/S0907444902006169 ]

Crystallization and preliminary X-ray crystallographic studies of monoacylglycerol lipase of the moderately thermophilic Bacillus sp. H-257

K. Yoneda, T. Nishimura, N. Katunuma, S. Imamura, K. Nitta and H. Tsuge

Synopsis: A thermostable monoacylglycerol lipase from the moderately thermophilic Bacillus sp. H-257 has been crystallized. Diffraction data have been collected to 2.6  A resolution.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1234-1236  [ doi:10.1107/S0907444902007965 ]

Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima

A. A. Krivenko, A. V. Kazantsev, C. Adamidi, D. J. Harrington and N. R. Pace

Synopsis: RNase P protein from T. maritima was overexpressed in E. coli, purified and crystallized. Crystals diffract beyond 2.0  Å, belong to the monoclinic space group P2₁ and have unit-cell parameters a = 56.29, b = 64.41, c = 68.19  Å, = 101.94°.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1237-1239  [ doi:10.1107/S0907444902008132 ]

Crystallization of the FAD-independent acetolactate synthase of Klebsiella pneumoniae

S. S. Pang, L. W. Guddat and R. G. Duggleby

Synopsis: The crystallization and preliminary X-ray diffraction analysis of K. pneumoniae acetolactate synthase is reported. This enzyme is involved in the formation of 2-acetolactate which is the precursor of the branched-chain amino acids valine and leucine.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1240-1242  [ doi:10.1107/S0907444902007679 ]

Expression, purification, crystallization and preliminary X-ray analysis of a DNA-binding protein from Methanococcus jannaschii

G. Wang, R. Guo, M. Bartlam, H. Xue, H. Yang, Y. Liu, L. Huang and Z. Rao

Synopsis: small DNA-binding protein of 87 amino-acid residues from the hyperthermophilic archaeon M. jannaschii (Mja10b) has been cloned and overexpressed in Escherichia coli.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1243-1245  [ doi:10.1107/S0907444902008326 ]

Crystallization and preliminary analysis of Escherichia coli YodA

G. David, K. Blondeau, M. Renouard and A. Lewit-Bentley

Synopsis: A protein of unknown function, YodA, from E. coli was purified and crystallized in several different crystal forms.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1246-1248  [ doi:10.1107/S0907444902007667 ]

Crystallization and preliminary structural analysis of an antibody complex formed with PfMSP1-19, a malaria vaccine candidate

J. C. Pizarro, V. Chitarra, C. Calvet, D. Verger and G. A. Bentley

Synopsis: The complex formed between PfMSP1-19, a promising malaria vaccine candidate, and the Fab of a specific monoclonal antibody has been crystallized. A preliminary model of the complex has been determined by molecular replacement.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1249-1251  [ doi:10.1107/S0907444902008338 ]

Characterization and crystallization of DivK, an essential response regulator for cell division and differentiation in Caulobacter crescentus

S. Cabantous, V. Guillet, N. Ohta, A. Newton and J.-P. Samama

Synopsis: The response regulator DivK was crystallized in space group P2₁2₁2₁, with unit-cell parameters a = 37.2, b = 40.5, c = 67.1  Å. Native data have been collected at 1.6  Å resolution.

Online 20 June 2002

 

Acta Cryst. (2002). D58, 1252-1254  [ doi:10.1107/S0907444902007333 ]

Anisotropic behaviour of the C-terminal Kunitz-type domain of the 3 chain of human type VI collagen at atomic resolution (0.9  Å)

B. Arnoux, A. Ducruix and T. Prangé

Synopsis: Anisotropic analysis of the C-term fragment of human collagen shows a high degree of libration in secondary structures at 100  K.

PDB reference: 1kth

Online 20 June 2002