Biological Crystallography

 

Acta Cryst. (2002). D58, 195-208  [ doi:10.1107/S0907444901019291 ]

A genetic algorithm for the identification of conformationally invariant regions in protein molecules

T. R. Schneider

Synopsis: A genetic algorithm is described that divides a protein into rigid and flexible parts by automatic analysis of an ensemble of conformers.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 209-214  [ doi:10.1107/S090744490101914X ]

Soaking: the effect of osmotic shock on tetragonal lysozyme crystals

F. J. López-Jaramillo, A. B. Moraleda, L. A. González-Ramírez, A. Carazo and J. M. García-Ruiz

Synopsis: The effect of osmotic shock on tetragonal lysozyme crystals is experimentally demonstrated. The network of channels and the charge of the crystal are responsible for a Gibbs-Donnan effect. This plays a critical role in the exchange of water, which leads to the formation of cracks.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 215-224  [ doi:10.1107/S090744490101959X ]

Combining image-seeking functions and a subtraction strategy: a vector-space procedure to improve many-body searches in molecular replacement

C. Álvarez-Rúa, J. Borge and S. García-Granda

Synopsis: The subtraction of the contribution of already positioned molecules from an observed Patterson map has proved to be useful for the determination of the correct orientation of the remaining molecules in the asymmetric unit of the crystal cell. For this purpose, a new procedure that incorporates a difference Patterson map in the evaluation of a vector-search rotation function has been developed.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 225-232  [ doi:10.1107/S090744490101993X ]

Crystal structure of equine apolactoferrin at 303  K providing further evidence of closed conformations of N and C lobes

P. Kumar, J. A. Khan, S. Yadav and T. P. Singh

Synopsis: The structure of equine apolactoferrin has been determined at 303  K. Both N and C lobes have been found in the closed conformations similar to those observed in various metal-saturated lactoferrin forms and in apolactoferrin at 277  K.

PDB reference: 1i6b

Online 24 January 2002

 

Acta Cryst. (2002). D58, 233-241  [ doi:10.1107/S0907444901020522 ]

A reassessment of the MAdCAM-1 structure and its role in integrin recognition

J. Dando, K. W. Wilkinson, S. Ortlepp, D. J. King and R. L. Brady

Synopsis: A second crystal structure of human mucosal addressin cell-adhesion molecule reveals that strand swapping can lead to dimer assembly and alters the conformation of the proposed integrin-binding surface.

PDB reference: 1gsm

Online 24 January 2002

 

Acta Cryst. (2002). D58, 242-249  [ doi:10.1107/S0907444901019576 ]

SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins

F. Merzel and J. C. Smith

Synopsis: A method for calculating small-angle X-ray and neutron scattering from atomic detail models of solvated macromolecules is presented. The method also derives an analytical surface of the macromolecule which reproduces explicit-atom profiles well.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 250-259  [ doi:10.1107/S0907444901018327 ]

Role of water molecules in the structure and function of aspartic proteinases

B. V. L. S. Prasad and K. Suguna

Synopsis: Conserved water molecules in the crystal structures of aspartic proteinases have been identified. Possible roles of these water molecules in the enzyme's structure and function have been analyzed.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 260-266  [ doi:10.1107/S0907444901018984 ]

Structure of Mycobacterium tuberculosis chaperonin-10 at 3.5  Å resolution

B. Taneja and S. C. Mande

Synopsis: The structural features of M. tuberculosis chaperonin-10 are reported and compared with the available chaperonin-10 structures. The structure also identifies binding sites for metal ions in the dome loop that have previously been shown to modulate the plastic states of M. tuberculosis chaperonin-10.

PDB reference: 1hx5

Online 24 January 2002

 

Acta Cryst. (2002). D58, 267-274  [ doi:10.1107/S0907444901019606 ]

Structure of the imipenem-hydrolyzing class A -lactamase SME-1 from Serratia marcescens

W. Sougakoff, G. L'Hermite, L. Pernot, T. Naas, V. Guillet, P. Nordmann, V. Jarlier and J. Delettré

Synopsis: The structure determination and site-directed mutagenesis of the imipenemase SME-1 reveal the peculiar organization of its active site and the importance of the disulfide bridge found in the active-site cavity of the enzyme.

PDB reference: 1dy6

Online 24 January 2002

 

Acta Cryst. (2002). D58, 275-283  [ doi:10.1107/S0907444901019710 ]

Methodology and applications of automatic electron-density map interpretation by six-dimensional rotational and translational search for molecular fragments

F. Pavelcik, J. Zelinka and Z. Otwinowski

Synopsis: A method which is able to locate fragments precisely over a wide range of resolutions for structure types from small organic molecules to proteins is described.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 284-291  [ doi:10.1107/S0907444901020133 ]

Reliable quality-control methods for protein crystal structures

J. Badger and J. Hendle

Synopsis: A set of quality standards that a fully refined protein structure should be able to meet is derived. Methods for detecting local structural errors are also evaluated and applied to a sample of recent structures from the Protein Data Bank.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 292-295  [ doi:10.1107/S090744490101808X ]

Crystallization and preliminary X-ray diffraction analysis of a novel pectate lyase from Azospirillum irakense

H. Novoa de Armas, A. Rabijns, C. Verboven, J. Desair, A. Vande Broek, J. Vanderleyden and C. De Ranter

Synopsis: The preliminary X-ray crystallographic characterization of PelA from A. irakense is reported. This enzyme defines a new class of pectate lyases as it displays no homology to other bacterial, plant or fungal pectinases of known published structure.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 296-298  [ doi:10.1107/S0907444901018741 ]

Crystallization and preliminary X-ray crystallographic analysis of p24, a component of the potato nuclear factor PBF-2

D. Desveaux, J. Allard, N. Brisson and J. Sygusch

Synopsis: The single-stranded DNA binding factor, PBF-2, is induced during pathogen infection of potato tubers and is implicated in defense gene regulation. Its DNA-binding component, p24, represents a conserved, ubiquitous family of plant-specific putative transcriptional regulators lacking strong similarity to proteins of known function.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 299-302  [ doi:10.1107/S0907444901018753 ]

Crystallization and low-resolution structure of an effector-caspase/P35 complex: similarities and differences to an initiator-caspase/P35 complex

M. J. Eddins, D. Lemongello, P. D. Friesen and A. J. Fisher

Synopsis: Baculovirus P35 is a protein that prevents apoptosis in a diverse range of organisms. P35 stoichiometrically inhibits the apoptotic caspases in a cleavage-dependant mechanism that involves formation of a tight complex. An insect effector-caspase/P35 complex has been crystallized and its low-resolution structure is compared with the human initiator-caspase/P35 structure.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 303-305  [ doi:10.1107/S0907444901018789 ]

Crystallization and preliminary X-ray crystallographic analysis of the Rv2002 gene product from Mycobacterium tuberculosis, a -ketoacyl carrier protein reductase homologue

J. K. Yang, H.-J. Yoon, H. J. Ahn, B. I. Lee, S. H. Cho, G. S. Waldo, M. S. Park and S. W. Suh

Synopsis: A soluble mutant (I6T/V47M/T69M) of the Rv2002 gene product (FabG3) of M. tuberculosis was crystallized. The X-ray diffraction quality of the crystal improved significantly after annealing/dehydration, enabling data collection to 1.8  Å resolution.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 306-309  [ doi:10.1107/S0907444901018832 ]

Pentaerythritol propoxylate: a new crystallization agent and cryoprotectant induces crystal growth of 2-methylcitrate dehydratase

A. M. Gulick, A. R. Horswill, J. B. Thoden, J. C. Escalante-Semerena and I. Rayment

Synopsis: The use of substituted pentaerythritol compounds as precipitants and cryoprotectants for protein crystallography is described. These agents exhibit properties that lie between MPD and PEG and expand the repertoire of precipitants available for crystal growth.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 310-311  [ doi:10.1107/S0907444901018959 ]

Crystallization and preliminary X-ray analysis of the DNA decamers d(CCGGATCCGG) and d(CCGGCGCCGG)

J. Aymami, J. Pous, J. N. Lisgarten and M. Coll

Synopsis: The DNA decamers d(CCGGATCCGG) and d(CCGGCGCCGG) have been crystallized in order to investigate the effects of changing the two central base pairs of the DNA fragment d(CCGGGACCGG). Previous studies have already demonstrated that the structure of the former DNA fragment contains a DNA Holliday junction.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 312-313  [ doi:10.1107/S0907444901018960 ]

Crystallization and preliminary X-ray analysis of the antimalarial and cytotoxic alkaloid cryptolepine complexed with the DNA fragment d(CCTAGG)₂

J. N. Lisgarten, J. Pous, M. Coll, C. W. Wright and J. Aymami

Synopsis: Crystals of the indoquinoline alkaloid cryptolepine complexed with the DNA fragment d(CCTAGG)₂ have been grown in order to investigate a possible new type of intercalation between equal base pairs.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 314-315  [ doi:10.1107/S090744490101962X ]

Crystallization of PNMT, the adrenaline-synthesizing enzyme, is critically dependent on a high protein concentration

J. Begun, M. J. McLeish, J. M. Caine, E. Palant, G. L. Grunewald and J. L. Martin

Synopsis: Human phenylethanolamine N-methyltransferase has been crystallized in a form suitable for structural studies. A major factor in obtaining crystals was the use of protein concentrations of greater than 90  mg  ml^-1.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 316-318  [ doi:10.1107/S0907444901019886 ]

Escherichia coli B -glutamylcysteine synthetase: modification, purification, crystallization and preliminary crystallographic analysis

T. Hibi, H. Hisada, T. Nakatsu, H. Kato and J. Oda

Synopsis: E. coli B -glutamylcysteine synthetase has been crystallized. Native data have been collected to 2.8  Å resolution.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 319-321  [ doi:10.1107/S0907444901019898 ]

Purification and preliminary crystallographic study of Trametes versicolor laccase in its native form

T. Bertrand, C. Jolivalt, E. Caminade, N. Joly, C. Mougin and P. Briozzo

Synopsis: A 2.4  Å resolution data set was collected from a crystal of T. versicolor laccase. The initial electron-density maps indicate the presence of all four Cu atoms involved in electron transfer.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 322-323  [ doi:10.1107/S0907444901019928 ]

Crystallization and preliminary X-ray diffraction analysis of creatine amidinohydrolase from Actinobacillus

B. Padmanabhan and M. Horikoshi

Synopsis: The homodimeric form of creatine amidinohydrolase from Actinobacillus has been crystallized by the hanging-drop vapour-diffusion method followed by macroseeding using PEG 6000 as a precipitant.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 324-326  [ doi:10.1107/S0907444901019989 ]

Crystallization and preliminary X-ray diffraction studies of -phosphoglucomutase from Lactococcus lactus

S. D. Lahiri, G. Zhang, P. Radstrom, D. Dunaway-Mariano and K. N. Allen

Synopsis: Two crystal forms of -phosphoglucomutase have been obtained in space group P2₁2₁2₁, with unit-cell parameters a = 53.67, b = 92.78, c = 111.60 and a = 53.21, b = 57.01, c = 76.11  Å. A complete three-wavelength MAD data set to 2.3  Å resolution has been collected from selenomethionine-substituted protein.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 327-329  [ doi:10.1107/S090744490102008X ]

Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein from Mycobacterium tuberculosis

K. Saikrishnan, J. Jeyakanthan, J. Venkatesh, N. Acharya, K. Purnapatre, K. Sekar, U. Varshney and M. Vijayan

Synopsis: The single-stranded DNA-binding protein from M. tuberculosis has been crystallized in a trigonal form and an orthorhombic form. A mercury derivative of the trigonal crystals has been prepared.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 330-332  [ doi:10.1107/S0907444901020091 ]

Crystallization and preliminary X-ray crystallographic studies on acyl-(acyl carrier protein) from Escherichia coli

A. Roujeinikova, C. Baldock, W. J. Simon, J. Gilroy, P. J. Baker, A. R. Stuitje, D. W. Rice, J. B. Rafferty and A. R. Slabas

Synopsis: Butyryl-ACP from E. coli, its selenomethionine (SeMet) variant and SeMet butyryl-ACP I62M have been crystallized. Crystals of the native protein and SeMet butyryl-ACP I62M belong to space group P2₁2₁2₁ and diffract to beyond 1.4  Å, whereas those of native SeMet butyryl-ACP belong to space group P6₃ and diffract to at least 2  Å.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 333-335  [ doi:10.1107/S0907444901020248 ]

Crystallization and preliminary X-ray data of the recombinant peptide amidase from Stenotrophomonas maltophilia

S. Neumann, J. Granzin, M.-R. Kula and J. Labahn

Synopsis: Crystals of peptide amidase from S. maltophilia, which selectively hydrolyses the C-terminal amide bond in peptide amides, have been obtained by sitting-drop vapour diffusion.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 336-338  [ doi:10.1107/S0907444901020236 ]

Crystallization and preliminary crystallographic analysis of a family 45 endoglucanase from the thermophilic fungus Melanocarpus albomyces

M. Hirvonen and A. C. Papageorgiou

Synopsis: 20K-cellulase, an endoglucanase from the thermophilic fungus M. albomyces, has been crystallized and full data were collected to 2.2  Å using synchrotron radiation. A methodology is described for growing single crystals of this endoglucanase.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 339-340  [ doi:10.1107/S0907444901020303 ]

Crystallization and preliminary X-ray crystallographic analysis of glutathione amide reductase from Chromatium gracile

B. Vergauwen, F. Van Petegem, H. Remaut, F. Pauwels and J. Van Beeumen

Synopsis: The successful crystallographic analysis of glutathione amide reductase crystals is presented, leading to an initial structure solution by a molecular-replacement strategy. Even though glutathione amide reductase displays an altered substrate as well as cofactor specificity, it is seen to be a structural glutathione reductase homologue.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 341-342  [ doi:10.1107/S090744490102039X ]

Crystallization and preliminary X-ray analysis of the membrane-bound cytochrome c nitrite reductase complex (NrfHA) from Wolinella succinogenes

O. Einsle, P. Stach, A. Messerschmidt, O. Klimmek, J. Simon, A. Kröger and P. M. H. Kroneck

Synopsis: The membrane-bound NrfHA complex from W. succinogenes has been purified and crystallized in space group I422. MAD data has been collected at the iron K edge.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 343-345  [ doi:10.1107/S0907444901020443 ]

Crystallization and preliminary X-ray analysis of the molybdenum-dependent pyrogallol-phloroglucinol transhydroxylase of Pelobacter acidigallici

D. J. Abt, O. Einsle, H. Niessen, R. Krieger, A. Messerschmidt, B. Schink and P. M. H. Kroneck

Synopsis: The molybdo-/iron-sulfur protein transhydroxylase was purified to homogeneity and crystals were grown which belong to space group P1. MAD data have been collected and structure solution is under way.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 346-348  [ doi:10.1107/S0907444901020406 ]

Preparation and crystallization of selenomethionyl dextranase from Penicillium minioluteum expressed in Pichia pastoris

A. M. Larsson, J. Ståhlberg and T. A. Jones

Synopsis: Dextranase has been expressed in P. pastoris with about 50% incorporation of selenomethionine. The enzyme has been crystallized in space group P2₁2₁2, with unit-cell parameters a = 103.6, b = 115.3, c = 49.8  Å and one molecule per asymmetric unit. The crystals diffract to 2.0  Å.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 349-351  [ doi:10.1107/S090744490102056X ]

Characterization of Escherichia coli OtsA, a trehalose-6-phosphate synthase from glycosyltransferase family 20

R. P. Gibson, R. M. Lloyd, S. J. Charnock and G. J. Davies

Synopsis: The trehalose-6-phosphase synthase, OtsA, a UDP-sugar dependent glycosyltransferase from Escherichia coli, has been cloned, overexpressed and crystallized in two forms suitable for X-ray diffraction studies.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 352-354  [ doi:10.1107/S0907444901020728 ]

Purification, crystallization and preliminary X-ray analysis of aspartokinase III from Escherichia coli

J. Blanco and R. E. Viola

Synopsis: Aspartokinases catalyze the commitment step in the aspartate biosynthetic pathway. Aspartokinase III has been crystallized, in complex with MgADP and aspartate, and diffraction data collected.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 355-358  [ doi:10.1107/S0907444901020753 ]

Crystallization and preliminary X-ray crystallographic studies on the parD-encoded protein Kid from Escherichia coli plasmid R1

D. Hargreaves, R. Giraldo, S. Santos-Sierra, R. Boelens, D. W. Rice, R. Díaz Orejas and J. B. Rafferty

Synopsis: The R1 plasmid-encoded toxic protein Kid from the parD system of E. coli has been overexpressed, purified, refolded and crystallized. Selenomethionine-incorporated crystals of Kid belong to space group P2₁, have unit-cell parameters a = 32.9, b = 45.0, c = 64.4  Å, = 96.2° and diffract to a d_min of better than 1.8  Å on a synchrotron-radiation source.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 359-361  [ doi:10.1107/S090744490102073X ]

Crystallization and preliminary X-ray diffraction studies of Escherichia coli branching enzyme

M. C. Abad, K. Binderup, J. Preiss and J. Geiger

Synopsis: Branching enzyme catalyzes the formation of the -1,6 branch points in glycogen. This paper reports the crystallization and X-ray diffraction data collected to a resolution of 2.3  Å.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 362-365  [ doi:10.1107/S0907444901020765 ]

Purification, crystallization and preliminary X-ray diffraction analysis of an archaeal ABC-ATPase

G. Verdon, S.-V. Albers, B. W. Dijkstra, A. J. M. Driessen and A.-M.W.H. Thunnissen

Synopsis: Two related crystal forms of an ABC-ATPase have been obtained in the absence of nucleotide. Experimental phases could be derived from single-wavelength anomalous diffraction data collected on an iodide derivative.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 366-369  [ doi:10.1107/S0907444901021035 ]

Strategies for the structural determination of the catalytic domain of Escherichia coli cytotoxic necrotizing factor 1

L. Buetow, G. Flatau, K. Chiu, P. Boquet and P. Ghosh

Synopsis: A combination of strategies leading to the successful structural determination of the catalytic domain of cytotoxic necrotizing factor 1 are presented. These strategies include successful expression of a partially soluble 33  kDa active CNF1 fragment, growth and optimization of crystals suitable for X-ray diffraction studies and determination of phases using a quadruple methionine-substitution mutant of the fragment.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 370-373  [ doi:10.1107/S0907444901021473 ]

Purification, crystallization and molecular symmetry of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis

E. M. Vogan, C. R. Bellamacina, X. He, B. M. Foxman, D. Ringe, H.-W. Liu and G. A. Petsko

Synopsis: Crystals of a recombinant form of CDP-D-glucose 4,6-dehydratase from Y. pseudotuberculosis have been grown in two crystal forms, both possessing pseudo-translational non-crystallographic symmetry.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 374-376  [ doi:10.1107/S0907444901021503 ]

Crystallization and preliminary X-ray structure determination of jack bean urease with a bound antibody fragment

L. Sheridan, C. M. Wilmot, K. D. Cromie, P. van der Logt and S. E. V. Phillips

Synopsis: Jack bean urease complexed with an antibody fragment has been crystallized, a partial 3.3  Å data set has been collected and a molecular-replacement solution for the urease has been determined.

Online 24 January 2002

 

Acta Cryst. (2002). D58, 377-379  [ doi:10.1107/S0907444901018972 ]

Structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45  Å resolution

G. Kolstad, B. Synstad, V. G. H. Eijsink and D. M. F. van Aalten

Synopsis: The refined high-resolution structure of the D140N mutant of chitinase B from S. marcescens sheds light on the roles of Asp140 and Asp142 during catalysis.

PDB reference: 1goi

Online 24 January 2002