Biological Crystallography

 

Acta Cryst. (2002). D58, 1255-1261  [ doi:10.1107/S0907444902008430 ]

Metal-free MIRAS phasing: structure of apo-S100A3

P. R. E. Mittl, G. Fritz, D. F. Sargent, T. J. Richmond, C. W. Heizmann and M. G. Grütter

Synopsis: Metal-free S100A3, a cysteine-rich Ca²⁺- and Zn²⁺-binding protein, has been crystallized by vapour diffusion under the strict exclusion of oxygen and in the absence of divalent metal ions. The structure was solved by MIRAS phasing using potassium iodide and xenon derivatives.

PDB reference: 1kso

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1262-1268  [ doi:10.1107/S0907444902009526 ]

X-ray-induced debromination of nucleic acids at the Br  K absorption edge and implications for MAD phasing

E. Ennifar, P. Carpentier, J.-L. Ferrer, P. Walter and P. Dumas

Synopsis: Multi-wavelength anomalous dispersion using brominated derivatives is considered a common and convenient technique for solving chemically synthesized nucleic acid structures. Here, it is shown that a relatively moderate X-ray dose can induce sufficient debromination to prevent structure determination.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1269-1276  [ doi:10.1107/S0907444902009599 ]

Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG

K. Saikrishnan, M. Bidya Sagar, R. Ravishankar, S. Roy, K. Purnapatre, P. Handa, U. Varshney and M. Vijayan

Synopsis: A comparative study involving the structures reported here and similar known structures show that the mobility of the UDG molecule consists of the rigid-body movement of the two domains that make up the molecule and the flexibility within the domains. DNA binding leads to domain closure, while association with the proteinaceous inhibitor does not.

PDB references: 1lqj, 1lqg and 1lqm

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1277-1281  [ doi:10.1107/S090744490200971X ]

Application of direct methods to protein crystallographic phase extension

F. Jiang

Synopsis: A new formulation of direct methods using the sign probability originally introduced for breaking the phase ambiguity has been proposed, in which the known phase information could be used as constrained phases in the phase refinement. This new formulation has been applied to protein crystallographic phase extension and shown to be effective.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1282-1286  [ doi:10.1107/S0907444902009794 ]

Fast rotational matching

J. A. Kovacs and W. Wriggers

Synopsis: A computationally efficient formulation is presented that significantly accelerates the rotational search in biomolecular matching problems. This is achieved by means of a new set of parameters that allows Fourier transformation of all three rotational degrees of freedom.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1287-1297  [ doi:10.1107/S090744490200999X ]

Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues

Y. Shen, S. Song and Z. Lin

Synopsis: The structures of GAPDH complexed with coenzyme analogues ADP-ribose and SNAD⁺ have been determined by molecular replacement. SNAD⁺-GAPDH reveals significant molecular asymmetry in the crystalline state.

PDB references: 1ihx and 1ihy

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1298-1306  [ doi:10.1107/S0907444902010016 ]

Structures of V45E and V45Y mutants and structure comparison of a variety of cytochrome  b₅ mutants

J.-H. Gan, J. Wu, Z.-Q. Wang, Y.-H. Wang, Z.-X. Huang and Z.-X. Xia

Synopsis: The structures of cytochrome  b₅ mutants V45E and V45Y reveal that the large side chains of Glu45 and Tyr45 of the mutants point to solvent instead of pointing to heme, leading to a decrease in the hydrophobicity of the heme pocket. The rotation of the porphyrin ring and the conformational change of the axial ligand His39 in the V45Y mutant indicate that the microenvironment of the heme is disturbed owing to the mutation.

PDB references: 1lqx and 1lr6

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1307-1313  [ doi:10.1107/S0907444902010090 ]

Atomic resolution data reveal flexibility in the structure of RNase Sa

J. Sevcík, V. S. Lamzin, Z. Dauter and K. S. Wilson

Synopsis: The structure of recombinant RNase Sa from 1.0  Å spacing synchrotron data collected at cryogenic temperature shows two alternative conformations of the main chain in two loops which contain active-site residues. This feature was not observed in the structure refined against room-temperature data at 1.2  Å resolution.

PDB reference: 1lni

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1314-1321  [ doi:10.1107/S0907444902010107 ]

Structure of -cinnamomin, a protein toxic to some plant species

M. L. Rodrigues, M. Archer, P. Martel, A. Jacquet, A. Cravador and M. A. Carrondo

Synopsis: The X-ray structure of an elicitin, -cinnamomin, secreted by the phytopathogenic fungus P. cinnamomi has been determined by the molecular-replacement method and refined to 1.8  Å resolution.

PDB reference: 1ljp

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1322-1328  [ doi:10.1107/S0907444902010156 ]

Structure of creatine amidinohydrolase from Actinobacillus

B. Padmanabhan, A. Paehler and M. Horikoshi

Synopsis: The crystal structure of creatine amidinohydrolase from Actinobacillus has been determined by the molecular-replacement method and refined to 2.7  Å resolution.

PDB reference: 1kp0

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1329-1331  [ doi:10.1107/S0907444902006170 ]

Purification, crystallization and preliminary X-ray analysis of the soluble domain of the Na⁺-pumping cytochrome bo quinol oxidase from Vitreoscilla

K.-J. Kim, Y. Kim, K.-W. Park, D. A. Webster and A. J. Howard

Synopsis: The 24  kDa CyoA soluble domain of Vitreoscilla cytochrome bo quinol oxidase has been crystallized from a solution of 2  M ammonium sulfate and 5% 2-propanol. The crystals belong to space group P4₃32 with a = 122.2  Å and contain one CyoA subunit per asymmetric unit.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1332-1334  [ doi:10.1107/S0907444902007953 ]

Crystallization and preliminary X-ray diffraction analysis of the trigonal crystal form of Saccharomyces cerevisiae alcohol dehydrogenase I: evidence for the existence of Zn ions in the crystal

K.-J. Kim and A. J. Howard

Synopsis: Saccharomyces cerevisiae alcohol dehydrogenase I crystallizes in space group P3₁21 or P3₂21 and diffracts to 3.0  Å resolution. A fluorescence scan of the crystal produced a peak at 9671.6  eV, suggesting the presence of Zn²⁺ ions in the crystal.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1335-1337  [ doi:10.1107/S0907444902010466 ]

Alliin lyase (alliinase) from garlic (Allium sativum): crystallization and preliminary X-ray characterization

L. J. W. Shimon, A. Rabinkov, T. Miron, D. Mirelman, M. Wilchek and F. Frolow

Synopsis: The enzyme alliinase has been isolated from garlic bulbs and crystallized. The crystals belong to space group P2₁, with unit-cell parameters a = 70.191, b = 127.006, c = 108.085  Å, = 93.384°.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1338-1339  [ doi:10.1107/S0907444902008478 ]

Crystallization and preliminary X-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1

M. W. Bhuiya, H. Tsuge, H. Sakuraba, K. Yoneda, N. Katunuma and T. Ohshima

Synopsis: Glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, A. pernix K1, has been crystallized. Diffraction data sets have been collected at 3.0  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1340-1342  [ doi:10.1107/S0907444902008958 ]

Crystallization and preliminary X-ray analysis of the TRAF domain of TRAF3

C.-Z. Ni, K. Welsh, J. Zheng, M. Havert, J. C. Reed and K. R. Ely

Synopsis: Crystallization conditions have been established to produce high-quality crystals of the TRAF domain of TNF-receptor-associated factor TRAF3 that are suitable for structural studies of the factor alone or in complex with peptides from the interacting regions of TNF receptors.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1343-1345  [ doi:10.1107/S0907444902009125 ]

A new crystal form of restriction endonuclease EcoRII that diffracts to 2.8  Å resolution

E. X. Zhou, M. Reuter, E. J. Meehan and L. Chen

Synopsis: A new crystal form of EcoRII, a type IIe restriction endonuclease, has been grown. Crystals of the new monoclinic form diffract to 2.8  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1346-1349  [ doi:10.1107/S0907444902009137 ]

A stepwise optimization of crystals of rhamnogalacturonan lyase from Aspergillus aculeatus

R. Kadirvelraj, P. Harris, J.-C.N. Poulsen, S. Kauppinen and S. Larsen

Synopsis: The stepwise optimization of crystallization conditions, characterization by X-ray diffraction and space-group changes upon heavy-atom derivatization of a rhamnogalacturonan lyase from A. aculeatus are reported.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1350-1352  [ doi:10.1107/S0907444902009150 ]

Crystallization and preliminary crystallographic analysis of the terminal oxygenase component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10

J.-W. Nam, Z. Fujimoto, H. Mizuno, H. Yamane, T. Yoshida, H. Habe, H. Nojiri and T. Omori

Synopsis: CarAa, the terminal oxygenase component of carbazole 1,9a-dioxygenase from P. resinovorans strain CA10, has been crystallized and diffraction data have been collected to 3.0  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1353-1355  [ doi:10.1107/S0907444902009162 ]

Crystallization and preliminary X-ray crystallographic studies of the PDZ domain of Shank1 from Rattus norvegicus

S. H. Park, Y. J. Im, S.-H. Rho, J. H. Lee, S. Yang, E. Kim and S. H. Eom

Synopsis: The PDZ domain of Shank1 from R. norvegicus has been crystallized in peptide-free form and in complex with the C-terminal octapeptide of GKAP. Native and complex crystals belong to space group P2₁ and P2₁2₁2₁ and diffract to 1.8 and 3.2  Å resolution, respectively.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1356-1358  [ doi:10.1107/S0907444902009447 ]

Crystallization and preliminary crystallographic analysis of creatininase from Pseudomonas putida

B. Beuth, K. Niefind and D. Schomburg

Synopsis: The creatinine-hydrolysing enzyme creatininase was crystallized successfully for the first time. The crystals diffract X-rays to at least 2.5  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1359-1361  [ doi:10.1107/S0907444902010004 ]

Crystallization and preliminary crystallographic analysis of the ezrin FERM domain

W. J. Smith and R. A. Cerione

Synopsis: The FERM domain of the cytoskeletal-plasma membrane linker molecule ezrin has been crystallized. The monoclinic crystals diffract to 2.3  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1362-1364  [ doi:10.1107/S0907444902010028 ]

Crystallization and preliminary X-ray diffraction studies of the transcriptional regulator TraR bound to its cofactor and to a specific DNA sequence

A. Vannini, C. Volpari, C. Gargioli, E. Muraglia, R. De Francesco, P. Neddermann and S. Di Marco

Synopsis: The transcriptional regulator TraR from A. tumefaciens has been crystallized in complex with its activating molecule, the pheromone N-3-oxooctanoyl-L-homoserine lactone (AAI), and with its target DNA sequence, an 18-base pair DNA sequence called TraBox. A three-wavelength MAD data set, using seleno-L-methionine-substituted crystals, has been collected to a resolution of 3  Å.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1365-1367  [ doi:10.1107/S090744490201003X ]

Overproduction, crystallization and preliminary X-ray diffraction analysis of a quinone oxidoreductase from Thermus thermophilus HB8

Y. Shimomura, K. Sumiguchi-Agari, R. Masui, S. Kuramitsu and K. Fukuyama

Synopsis: Quinone oxidoreductase from T. thermophilus HB8 was overproduced in E. coli and then crystallized in the absence and presence of NADPH.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1368-1370  [ doi:10.1107/S0907444902010120 ]

Purification, crystallization and preliminary X-ray analysis of the plectin actin-binding domain

L. Urbániková, L. Janda, A. Popov, G. Wiche and J. Sevcík

Synopsis: The actin-binding domain of plectin, a cytolinker protein, was expressed, purified and crystallized. Monoclinic crystals diffracted to 2.0  Å resolution using synchrotron radiation.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1371-1373  [ doi:10.1107/S0907444902010132 ]

Crystallization and preliminary X-ray analysis of the matrix protein of Borna disease virus

I. Kraus, H. Scheffczik, M. Eickmann, S. Kiermayer, M. T. Stubbs and W. Garten

Synopsis: The 16  kDa matrix protein of the Borna disease virus envelope expressed in E. coli crystallizes in the space group I432, with unit-cell parameters a = b = c = 144.6  Å. The crystals diffract to 3.1  Å.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1374-1375  [ doi:10.1107/S0907444902010168 ]

Crystallization and preliminary X-ray crystallographic studies of rice -galactosidase

Z. Fujimoto, O. Kobayashi, S. Kaneko, M. Momma, H. Kobayashi and H. Mizuno

Synopsis: -Galactosidases catalyze the hydrolysis of galactooligosaccharides and galactopolysaccharides to -galactose residues. -Galactosidase from rice (O. sativa L. ssp. japonica) was crystallized and X-ray data were collected at 1.9  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1376-1378  [ doi:10.1107/S0907444902010429 ]

Crystallization of the 43  kDa ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin

V. Lamour, L. Hoermann, J.-M. Jeltsch, P. Oudet and D. Moras

Synopsis: The 43  kDa ATPase domain of T. thermophilus gyrase B was overproduced in Escherichia coli and a three-step purification protocol yielded large quantities of highly purified enzyme which remained stable for weeks. Crystals of the 43  kDa domain in complex with novobiocin, one of the most potent inhibitors of bacterial topoisomerases, were obtained.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1379-1380  [ doi:10.1107/S0907444902008156 ]

Crystallization and preliminary crystallographic analysis of human L-xylulose reductase

O. El-Kabbani, R.P.-T. Chung, S. Ishikura, N. Usami, J. Nakagawa and A. Hara

Synopsis: Orthorhombic crystals of human L-xylulose reductase were grown from buffered polyethylene glycol solutions and diffract to 2.1  Å resolution.

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1381-1384  [ doi:10.1107/S090744490200896X ]

Structure of d(TGCGCA)₂ at 293  K: comparison of the effects of sequence and temperature

S. Thiyagarajan, P. Satheesh Kumar, S. S. Rajan and N. Gautham

Synopsis: The crystal structure of a hexameric DNA fragment with the sequence d(TGCGCA)₂ has been solved and refined at 293  K at a resolution of 1.64  Å. A comparison of the present structure with that at low temperature and with that of d(CGCGCG)₂ throws light on the effects of the sequence and of temperature on the duplex structure of Z-DNA hexamers.

NDB reference: zd0007

Online 20 July 2002

 

Acta Cryst. (2002). D58, 1385-1386  [ doi:10.1107/S090744490200985X ]

PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file

A. S. Z. Hussain, V. Shanthi, S. S. Sheik, J. Jeyakanthan, P. Selvarani and K. Sekar

Synopsis: A World Wide Web-based graphical user interface has been developed to manipulate the protein structures available in the Protein Data Bank.

Online 20 July 2002