Biological Crystallography

 

Acta Cryst. (2004). D60, 1509-1511  [ doi:10.1107/S0907444904018189 ]

Carl-Ivar Brändén (1934-2004)

J. Smith

Synopsis: Obituary for Carl-Ivar Brändén.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1512-1518  [ doi:10.1107/S0907444904014593 ]

Structure of DsbC from Haemophilus influenzae

M. Zhang, A. F. Monzingo, L. Segatori, G. Georgiou and J. D. Robertus

Synopsis: DsbC forms a flexible dimer that can accommodate a wide variety of protein substrates for disulfide-bond isomerization.

PDB reference: 1t3b

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1519-1526  [ doi:10.1107/S0907444904014969 ]

Ab initio phasing based on topological restraints: automated determination of the space group and the number of molecules in the unit cell

L. Urzhumtseva, N. Lunina, A. Fokine, J.-P. Samama, V. Y. Lunin and A. Urzhumtsev

Synopsis: Dependence of ab initio connectivity-based phasing on its principal parameters allows an automated indication of the space group and of the number of molecules in the unit cell.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1527-1534  [ doi:10.1107/S0907444904015094 ]

Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B

A. K. Pedersen, G. H. Peters, K. B. Møller, L. F. Iversen and J. S. Kastrup

Synopsis: The crystal structure of apo protein tyrosine phosphatase 1B has been determined to 1.95 Å resolution. The structure shows four highly coordinated water molecules in the active site of the enzyme and the WPD-loop in a closed conformation.

PDB reference: 1sug

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1535-1544  [ doi:10.1107/S0907444904015252 ]

Accurate automatic protein models

F. Pavelcik

Synopsis: Main-chain molecular fragments are positioned in electron density by a phased rotation and translation function. The fragments are refined as flexible generalized atoms and connected into chains. The sequence is aligned and side chains are built. The overall accuracy of the protein model is about 0.2 Å at a resolution of 1.2-1.9 Å.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1545-1554  [ doi:10.1107/S0907444904015422 ]

Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

X. Qiu and C. A. Janson

Synopsis: To demonstrate a new strategy for engineering crystal lattices through metal-mediated interactions, apo acyl carrier protein has been crystallized in the presence of zinc ions. The structure was solved with MAD phasing using zinc anomalous signals.

PDB reference: 1t8k

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1555-1561  [ doi:10.1107/S0907444904015628 ]

Ligand-binding and metal-exchange crystallographic studies on shrimp alkaline phosphatase

M. M. E. de Backer, S. McSweeney, P. F. Lindley and E. Hough

Synopsis: Shrimp alkaline phosphatase has been subjected to inhibitor and metal-exchange studies, which induced conformational changes in the active site.

PDB references: 1shn and 1shq

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1562-1568  [ doi:10.1107/S0907444904015732 ]

Statistical experimental design of protein crystallization screening revisited

T. T. Tran, I. Sorel and A. Lewit-Bentley

Synopsis: A statistical design approach is proposed to screen for and optimize protein crystallization conditions.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1569-1578  [ doi:10.1107/S0907444904016798 ]

Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni

R. M. F. Cardoso, C. H. T. P. Silva, A. P. Ulian de Araújo, T. Tanaka, M. Tanaka and R. C. Garratt

Synopsis: The crystal structure of the first human parasite superoxide dismutase is described. Alternate positions for the catalytic copper are described along with differences within the electrostatic loops used for substrate guidance.

PDB references: 1to4 and 1to5

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1579-1585  [ doi:10.1107/S0907444904016786 ]

Observation of time-resolved structural changes by linear interpolation of highly redundant X-ray diffraction data

J. Wang and S. E. Ealick

Synopsis: Linear interpolation of X-ray intensities from redundant data sets was used to determine the structures of insulin at different time points throughout the data collection. The structures reveal time-dependent structural changes that result from radiation exposure.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1586-1590  [ doi:10.1107/S090744490401697X ]

A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A₂ at 1.6 Å resolution using sulfur-SAS at 1.54 Å wavelength

K. Sekar, V. Rajakannan, D. Velmurugan, T. Yamane, R. Thirumurugan, M. Dauter and Z. Dauter

Synopsis: The crystal structure of the triple mutant (K53,56,120M) of a small protein (14 kDa), bovine pancreatic phospholipase A₂, has been redetermined using sulfur single-wavelength anomalous scattering (S-SAS) at 1.6 Å resolution using a wavelength of 1.54 Å.

PDB reference: 1vkq

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1591-1599  [ doi:10.1107/S0907444904017597 ]

Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2

J. Phan, J. E. Tropea and D. S. Waugh

Synopsis: The structure of the type III secretion chaperone SycH from Y. pestis has been solved in complex with a stable fragment of YscM2, a negative regulator of type III secretion.

PDB reference: 1ttw

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1600-1605  [ doi:10.1107/S0907444904015240 ]

Structure of serine acetyltransferase from Haemophilus influenzae Rd

J. Gorman and L. Shapiro

Synopsis: The structure of serine acetyltransferase from H. influenzae Rd determined at 2.7 Å resolution is presented. The structure is a hexamer consisting of a dimer of trimers, each of which contains subunits characterized by a conserved N-terminal -helical domain and a C-terminal left-handed parallel -helix.

PDB reference: 1s80

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1606-1610  [ doi:10.1107/S0907444904017603 ]

Structural genomics of Caenorhabditis elegans: structure of the BAG domain

J. Symersky, Y. Zhang, N. Schormann, S. Li, R. Bunzel, P. Pruett, C.-H. Luan and M. Luo

Synopsis: The crystal structure of BAG-1 protein from C. elegans reveals a new BAG-domain fold.

PDB reference: 1t7s

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1611-1613  [ doi:10.1107/S0907444904015033 ]

Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli

M. N. Vassylyeva, A. A. Perederina, V. Svetlov, S. Yokoyama, I. Artsimovitch and D. G. Vassylyev

Synopsis: Transcription factor DksA from E. coli, which contains a canonical Zn-finger motif, was cloned expressed, purified and crystallized. The crystals diffract beyond 2.0 Å resolution at a synchrotron and three complete multiple anomalous dispersion data sets were collected at the absorption edge of the Zn atom.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1614-1617  [ doi:10.1107/S0907444904015343 ]

Cloning, expression, crystallization and initial crystallographic analysis of the C-terminal domain of the amyloid precursor protein APP

C. Keil, R. Huber, W. Bode and M. E. Than

Synopsis: The C-terminal domain CAPPD of the -amyloid precursor protein, a type I transmembrane protein involved in Alzheimer's disease, was cloned, expressed in E. coli and, after purification, also crystallized. The initial electron-density map was of good quality and showed mostly helical regions.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1618-1621  [ doi:10.1107/S090744490401666X ]

Expression, purification, crystallization and preliminary X-ray diffraction studies of the cmcI component of Streptomyces clavuligerus 7-cephem-methoxylase

D. R. Lester, L. M. Öster, M. Svenda and I. Andersson

Synopsis: The expression, purification, crystallization and preliminary X-ray diffraction studies of the gene product of cmcI from S. clavuligerus is reported. CmcI is believed to control the conversion of cephalosporins to cephamycins via 7-methoxylation.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1622-1624  [ doi:10.1107/S090744490401515X ]

Crystallization and preliminary X-ray analysis of carboxypeptidase Y inhibitor I^C complexed with the cognate proteinase

J. Mima, M. Hayashida, T. Fujii, Y. Hata, R. Hayashi and M. Ueda

Synopsis: Carboxypeptidase Y inhibitor I^C, complexed with the cognate proteinase, was crystallized and X-ray diffraction data were collected to 2.7 Å resolution.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1625-1627  [ doi:10.1107/S0907444904015276 ]

Crystallization of a non-B and a B mutant HIV protease

M. Sanches, N. Helena Martins, A. Calazans, R. de Moraes Brindeiro, A. Tanuri, O. Augusto Ceva Antunes and I. Polikarpov

Synopsis: Two new HIV proteases isolated from Brazilian patients failing intensive anti-AIDS therapy, namely subtype B mutant and subtype F wild type protein, were crystallized. The crystallization procedure and the molecular replacement solution for both proteins are presented in this paper.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1628-1631  [ doi:10.1107/S0907444904015380 ]

Purification, crystallization and preliminary crystallographic data of the m₃G cap-binding domain of human snRNP import factor snurportin 1

A. Strasser, A. Dickmanns, U. Schmidt, E. Penka, H. Urlaub, M. Sekine, R. Lührmann and R. Ficner

Synopsis: Full-length SPN1 did not crystallize, so fragments with m₃G cap binding activity were generated by protease cleavage. The crystals of a 26 kDa fragment which were obtained had to be enlarged by two rounds of microseeding.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1632-1635  [ doi:10.1107/S0907444904015872 ]

Biochemical, biophysical and preliminary X-ray crystallographic analyses of the fusion core of Sendai virus F protein

X. Wang, Y. Xu, D. K. Cole, Z. Lou, Y. Liu, Z. Rao, M. Wang and G. F. Gao

Synopsis: The Sendai virus fusion-core six-helix bundle assembly was crystallized; crystals diffract X-rays to 2.5 Å resolution.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1636-1638  [ doi:10.1107/S0907444904017627 ]

Crystallization and preliminary X-ray analyses of desulfurization enzyme DszB and its C27S mutant complexed with biphenyl-2-sulfinic acid

W. C. Lee, T. Ohshiro, T. Matsubara, Y. Izumi and M. Tanokura

Synopsis: Crystallization and preliminary X-ray analyses of desulfurization enzyme DszB were conducted.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1639-1640  [ doi:10.1107/S0907444904016245 ]

Crystallization and preliminary X-ray diffraction analysis of HeLp, a heme lipoprotein from the hemolymph of the cattle tick Boophilus microplus

L. R. Alves, P. L. Oliveira, J. A. R. G. Barbosa, B. G. Guimarães and F. J. Medrano

Synopsis: The main protein from the hemolymph of the cattle tick B. microplus has been crystallized using 1,6-hexanediol. The crystals belonged to the triclinic space group P1 and diffracted up to 2.1 Å resolution.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1641-1643  [ doi:10.1107/S0907444904016403 ]

Crystallization and preliminary X-ray analysis of Escherichia coli MutT in binary and ternary complex forms

T. Nakamura, T. Doi, M. Sekiguchi and Y. Yamagata

Synopsis: E. coli MutT was crystallized in binary and ternary complex forms. The crystals diffracted to 1.96 and 2.56 Å resolution, respectively.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1644-1646  [ doi:10.1107/S0907444904016695 ]

Crystallization and preliminary X-ray analysis of heparinase II from Pedobacter heparinus

D. Shaya, Y. Li and M. Cygler

Synopsis: The crystallization and preliminary X-ray analysis of heparinase II from P. heparinus is reported. Heparinases from P. heparinus are widely used in medical and analytical applications; however, their three-dimensional structures and detailed catalytic mechanisms have yet to be determined.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1647-1650  [ doi:10.1107/S0907444904015185 ]

Purification, crystallization and preliminary X-ray analysis of Triatoma virus (TrV) from Triatoma infestans

G. S. Rozas-Dennis, G. Squires, J. Pous, M. D. Costabel, J. Lepault, J. Navaza, F. A. Rey and D. M. A. Guérin

Synopsis: Triatoma virus (TrV) is a viral pathogen of blood-sucking reduviid bugs (triatomines). This work describes the purification of TrV particles from infected T. infestans and their crystallization and preliminary crystallographic analyses.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1651-1653  [ doi:10.1107/S0907444904016701 ]

Expression, purification and preliminary crystallographic studies of human coactosin-like protein

L. Liu, Y. Wang, P. Zhang, Z. Cheng, M. Wan, Z. Zhou and W. Gong

Synopsis: Human coactosin-like protein has been expressed in high yield and the His-tagged protein was purified by affinity chromatography. Several different crystal forms were obtained by the hanging-drop vapour-diffusion method.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1654-1657  [ doi:10.1107/S0907444904016841 ]

Crystallization and preliminary crystallographic studies of the cofactor-binding domain of the LysR-type transcriptional regulator Cbl from Escherichia coli

E. Stec, M. Witkowska, M. M. Hryniewicz, A. M. Brzozowski, A. J. Wilkinson and G. D. Bujacz

Synopsis: The cofactor-binding domain of the LysR-type transcriptional regulator Cbl from E. coli has been cloned, overexpressed, purified and crystallized. The crystals diffract to 3.0 Å resolution using synchrotron radiation.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1658-1661  [ doi:10.1107/S0907444904016968 ]

Crystallization of the xeroderma pigmentosum group F endonuclease from Aeropyrum pernix

J. Lally, M. Newman, J. Murray-Rust, A. Fadden, Y. Kawarabayasi and N. McDonald

Synopsis: Three different crystal forms of apXPF were grown in trigonal, monoclinic and triclinic systems. The trigonal crystals diffracted to 2.8 Å and were grown in the presence of double-stranded DNA. Monoclinic crystals were grown without DNA and diffracted to 3.2 Å. Triclinic crystals were grown from a truncated apXPF protein lacking the tandem helix-hairpin-helix motifs and diffracted to 2.1 Å.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1662-1664  [ doi:10.1107/S0907444904017329 ]

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria

S. Dwivedi, S. P. Kruparani and R. Sankaranarayanan

Synopsis: The N-terminal module of an archaebacterial threonyl-tRNA synthetase responsible for editing function has been crystallized in P3₁₍₂₎21 space group.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1665-1667  [ doi:10.1107/S0907444904017561 ]

Expression, purification, crystallization and preliminary X-ray diffraction analysis of conjugated bile salt hydrolase from Bifidobacterium longum

R. S. Kumar, J. A. Brannigan, A. Pundle, A. Prabhune, G. G. Dodson and C. G. Suresh

Synopsis: Two different crystal forms have been obtained of the conjugated bile salt hydrolase from B. longum and their preliminary crystallographic characterization has been carried out.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1668-1669  [ doi:10.1107/S0907444904016051 ]

Crystals of X29, a Xenopus laevis U8 snoRNA-binding protein with nuclear decapping activity

B. A. Peculis, J. N. Scarsdale and H. T. Wright

Synopsis: X29, a nuclear Nudix hydrolase that binds and decaps U8 snoRNA, has been expressed in high yield and crystallized in a form that diffracts to 2.1 Å resolution.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1670-1673  [ doi:10.1107/S0907444904010972 ]

Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins

J. Jancarik, R. Pufan, C. Hong, S.-H. Kim and R. Kim

Synopsis: A solubility screen for determining the best solvent condition for a particular protein prior to crystallization trials is presented.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1674-1678  [ doi:10.1107/S090744490401844X ]

A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1

B. K. Collins, S. J. Tomanicek, N. Lyamicheva, M. W. Kaiser and T. C. Mueser

Synopsis: A solubility screen has been utilized to optimize initial crystallization results of A. pernix flap endonuclease-1.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1679-1682  [ doi:10.1107/S0907444904015215 ]

APRV - a program for automated data processing, refinement and visualization

M. Kroemer, M. K. Dreyer and K. U. Wendt

Synopsis: APRV is a program that automates routine procedures in high-throughput protein-ligand complex structure determination.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1683-1686  [ doi:10.1107/S0907444904015835 ]

MAD phasing: choosing the most informative wavelength combination

M. C. Burla, B. Carrozzini, G. L. Cascarano, C. Giacovazzo, M. Moustiakimov, G. Polidori and D. Siliqi

Synopsis: An algorithm for predicting the most informative wavelength combination in the MAD case is described.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1687-1690  [ doi:10.1107/S0907444904015896 ]

Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 Å resolution

E. L. Wise, J. Akana, J. A. Gerlt and I. Rayment

Synopsis: The X-ray crystal structure of D-ribulose 5-phosphate 3-epimerase (RPE) from Synechocystis reveals that the enzyme shares a highly conserved active site with other RPEs.

PDB reference: 1tqj

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1691-1693  [ doi:10.1107/S0907444904017615 ]

CLIMS: Crystallography Laboratory Information Management System

K. F. Fulton, S. Ervine, N. Faux, R. Forster, R. A. Jodun, W. Ly, L. Robilliard, J. Sonsini, D. Whelan, J. C. Whisstock and A. M. Buckle

Synopsis: CLIMS is a laboratory-information management system for protein crystallography that features a novel graphical interface to a relational database and assists all aspects of protein crystallization projects.

Online 26 August 2004

 

Acta Cryst. (2004). D60, 1694  [ doi:10.1107/S0907444904019134 ]

Two orthorhombic crystal structures of a galactose-specific lectin from Artocarpus hirsuta in complex with methyl--D-galactose. Addendum

K. N. Rao, C. G. Suresh, U. V. Katre, S. M. Gaikwad and M. I. Khan

Synopsis: Addendum to the paper by Rao et al. (2004), Acta Cryst. D60, 1404-1412.

PDB references: 1toq and 1tp8

Online 26 August 2004