Biological Crystallography

 

Acta Cryst. (2003). D59, 1533-1538  [ doi:10.1107/S0907444903013027 ]

The influence of an internal electric field upon protein crystallization using the gel-acupuncture method

N. Mirkin, B. A. Frontana-Uribe, A. Rodríguez-Romero, A. Hernández-Santoyo and A. Moreno

Synopsis: The influence of an internal electric field upon the protein structure of crystals grown inside capillary tubes is evaluated during the crystallization process by means of the gel-acupuncture method using lysozyme and thaumatin.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1539-1544  [ doi:10.1107/S0907444903013131 ]

Structure of pteridine reductase (PTR1) from Leishmania tarentolae

H. Zhao, T. Bray, M. Ouellette, M. Zhao, R. A. Ferre, D. Matthews, J. M. Whiteley and K. I. Varughese

Synopsis: The crystal structure of PTR1 from L. tarentolae as a binary complex with NADPH at 2.8  Å resolution has been solved by molecular-replacement techniques using the recently reported L. major PTR1 structure as a search model.

PDB reference: 1p33

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1545-1550  [ doi:10.1107/S0907444903014161 ]

Auracyanin B structure in space group P6₅

M. Lee, M. J. Maher, H. C. Freeman and J. M. Guss

Synopsis: A new crystal form of auracyanin B, a `blue' copper protein from the thermophilic green photosynthetic bacterium C. aurantiacus, has been refined at 1.9  Å resolution.

PDB reference: 1ov8

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1551-1556  [ doi:10.1107/S090744490301429X ]

Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7  Å resolution

S. Datta, T. Ikeda, K. Kano and F. S. Mathews

Synopsis: The binding site for phenylhydrazine in the quinohemoprotein amine dehydrogenase has been identified as the C6 position of the redox cofactor cysteine tryptophylquinone. This result firmly establishes C6 as the site of Schiff-base formation during catalytic turnover of this enzyme.

PDB reference: 1pby

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1557-1566  [ doi:10.1107/S0907444903014367 ]

Estimation of weights and validation: a marginal likelihood approach

A. A. Lebedev, I. J. Tickle, R. A. Laskowski and D. S. Moss

Synopsis: An estimator of weights for restrained macromolecular refinement is proposed which is based on an approximation of a marginal likelihood function of the weighting parameters and which uses all the X-ray data.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1567-1573  [ doi:10.1107/S0907444903014562 ]

Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin

I. Le Trong, S. Freitag, L. A. Klumb, V. Chu, P. S. Stayton and R. E. Stenkamp

Synopsis: Mutation of residues in streptavidin capable of hydrogen bonding to biotin causes significant changes in the binding constants for this protein/ligand system. Structure analyses show few changes in the three-dimensional structures of biotin complexes with the mutated proteins.

PDB references: 1n4j, 1n43, 1n7y, 1n9y, 1n9m, 1nbx, 1nc9, 1swu and 1ndj

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1574-1581  [ doi:10.1107/S0907444903014598 ]

Structure of a king cobra phospholipase A₂ determined from a hemihedrally twinned crystal

S. Xu, L. Gu, Q. Wang, Y. Shu, S. Song and Z. Lin

Synopsis: The 2.1  Å resolution structure of a king cobra PLA₂ was determined by molecular replacement from a perfectly hemihedrally twinned crystal and compared with the structure of a homologous PLA₂ from the same venom.

PDB reference: 1m8t

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1582-1588  [ doi:10.1107/S0907444903014604 ]

Structure of Rhodoferax fermentans high-potential iron-sulfur protein solved by MAD

A. González, S. Benini and S. Ciurli

Synopsis: This paper describes the structure solution and the resultant model of R. fermentans HiPIP, a bacterial iron-sulfur protein with high reduction potential.

PDB reference: 1hlq

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1589-1596  [ doi:10.1107/S0907444903014719 ]

Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics

J. Komoto, Y. Takata, T. Yamada, K. Konishi, H. Ogawa, T. Gomi, M. Fujioka and F. Takusagawa

Synopsis: A crystal structure of guanidinoacetate methyltransferase in a monoclinic modification was determined in which three of four subunits have a catalytically unfavorable loop containing Tyr136. From analysis of the Gd ion-binding site, characteristic features of Gd-ion binding have been revealed and may be useful for preparing heavy-atom derivatives for phasing.

PDB references: 1p1b and 1p1c

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1597-1602  [ doi:10.1107/S0907444903014902 ]

High-resolution structure of phenol hydroxylase and correction of sequence errors

C. Enroth

Synopsis: New diffraction data for phenol hydroxylase have been collected. Refinement to 1.7  Å resolution resulted in a final free R factor of 18.0%. The model was also corrected for 11 earlier sequencing errors.

PDB reference: 1pn0

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1603-1609  [ doi:10.1107/S0907444903014963 ]

Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase

V. Cody, J. R. Luft, W. A. Pangborn and A. Gangjee

Synopsis: Structural data are reported for the first example of the potent antifolate inhibitor 2,4-diamino-5-methyl-6-[(3',4',5'-trimethoxy-N-methylanilino)methyl]pyrido[2,3-d]pyrimidine (1) in complex with human dihydrofolate reductase (hDHFR) and NADPH.

PDB references: 1pd8, 1pd9 and 1pdb

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1610-1618  [ doi:10.1107/S0907444903014975 ]

Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method

T. Nakai, J. Ishijima, R. Masui, S. Kuramitsu and N. Kamiya

Synopsis: Because of the large number of molecules within a closely packed unit cell, this structure was solved by six-dimensional molecular replacement. Comparison with its counterpart from pea reveals highly conserved regions that are likely to be involved in intermolecular interactions.

PDB reference: 1onl

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1619-1627  [ doi:10.1107/S0907444903015130 ]

Automatic classification of sub-microlitre protein-crystallization trials in 1536-well plates

C. A. Cumbaa, A. Lauricella, N. Fehrman, C. Veatch, R. Collins, J. R. Luft, G. DeTitta and I. Jurisica

Synopsis: A technique for automatically evaluating microbatch (sub-microlitre drop) protein crystallization trials is described.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1628-1631  [ doi:10.1107/S0907444903016779 ]

Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein

V. Campanacci, M.-P. Egloff, S. Longhi, F. Ferron, C. Rancurel, A. Salomoni, C. Durousseau, F. Tocque, N. Brémond, J. C. Dobbe, E. J. Snijder, B. Canard and C. Cambillau

Synopsis: A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. Here, the cloning, E. coli expression, purification, and crystallization of the SARS-CoV Nsp9 protein, the first SARS-CoV protein to be crystallized, are reported.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1632-1634  [ doi:10.1107/S0907444903013660 ]

Crystallization of the chaperonin GroEL-GroES complex from Thermus thermophilus HB8

T. Shimamura, A. Koike-Takeshita, K. Yokoyama, M. Yoshida, H. Taguchi and S. Iwata

Synopsis: The native GroEL-GroES complex was isolated from T. thermophilus HB8 and crystallized. The triclinic crystal diffracted to 3.0  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1635-1636  [ doi:10.1107/S090744490301415X ]

Crystallization and preliminary crystallographic study of rBmKIT1, a recombinant -insect toxin from the scorpion Buthus martensii Karsch

Y. Huang, Q. Huang, H. Chen, Y. Tang, H. Miyake and M. Kusunoki

Synopsis: An -insect toxin from the scorpion B. martensii Karsch has been expressed, purified and crystallized.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1637-1639  [ doi:10.1107/S0907444903014100 ]

Crystallization and preliminary X-ray diffraction studies of aclacinomycin-10-methyl esterase and aclacinomycin-10-hydroxylase from Streptomyces purpurascens

A. Jansson, J. Niemi, P. Mäntsälä and G. Schneider

Synopsis: Crystals suitable for structure determination of two enzymes in the biosynthesis pathway of anthracyclines in Streptomyces, aclacinomycin-10-methyl esterase and aclacinomycin-10-hydroxylase, have been grown.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1640-1641  [ doi:10.1107/S0907444903014112 ]

Crystallization and preliminary X-ray crystallographic studies of phosphoenolpyruvate carboxykinase from Corynebacterium glutamicum

S. Aich, F. Imabayashi and L. T. J. Delbaere

Synopsis: Phosphoenolpyruvate carboxykinase (PCK) is a key enzyme involved in the regulation of gluconeogenesis. C. glutamicum PCK has been crystallized and X-ray diffraction data have been collected to 2.8  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1642-1644  [ doi:10.1107/S090744490301463X ]

Purification, crystallization and preliminary X-ray studies of ClpX from Helicobacter pylori

D. Y. Kim, C. A. Wu, D. R. Kim, S. C. Ha, Y.-H. Han and K. K. Kim

Synopsis: ClpX from H. pylori has been overexpressed, purified and crystallized. The crystals diffracted to 2.6  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1645-1647  [ doi:10.1107/S0907444903014641 ]

Overproduction, crystallization and preliminary X-ray diffraction analysis of probable ATP sulfurylase from Thermus thermophilus HB8

Y. Taguchi, J. Hoseki, Y. Kakuta and K. Fukuyama

Synopsis: A probable ATP sulfurylase from T. thermophilus HB8 was overexpressed in E. coli and crystallized in the presence of adenosine-5'-phosphosulfate.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1648-1650  [ doi:10.1107/S0907444903014616 ]

Purification, crystallization and preliminary X-ray crystallographic analysis of nucleoside diphosphate kinase from rice

J.-Y. Huang, C.-Y. Chang, T. Chang and C.-J. Chen

Synopsis: Crystals of nucleoside diphosphate kinase from rice have been obtained.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1651-1652  [ doi:10.1107/S0907444903014720 ]

Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8

M. N. Vassylyeva, H. Sakai, T. Matsuura, S. Sekine, M. Nishiyama, T. Terada, M. Shirouzu, S. Kuramitsu, D. G. Vassylyev and S. Yokoyama

Synopsis: LysX protein, involved in the lysine-biosynthesis pathway in T. thermophilus, was cloned, expressed, purified and crystallized. Complete diffraction data sets were collected for the two crystal forms at 2.5 and 3.1  Å resolution. Structure determination is now in progress.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1653-1655  [ doi:10.1107/S0907444903014896 ]

Coenzyme F₄₂₀-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms

C. H. Hagemeier, S. Shima, E. Warkentin, R. K. Thauer and U. Ermler

Synopsis: Methanogenic F₄₂₀-dependent methylene-H4MPT dehydrogenase has been expressed, purified and crystallized.  Crystals of selenomethionine-labelled enzyme diffracted to 1.5  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1656-1658  [ doi:10.1107/S0907444903015026 ]

X-ray crystallographic characterization and phasing of an NtrC homologue

L. Sallai, J. Hendle and P. A. Tucker

Synopsis: A two-domain construct of ZraR (HydG) response regulator from S. typhimurium has been crystallized and diffraction data have been recorded to 3.0  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1659-1661  [ doi:10.1107/S0907444903015397 ]

Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima

Ihsanawati, T. Kumasaka, T. Kaneko, C. Morokuma, S. Nakamura and N. Tanaka

Synopsis: Hyperthermophilic xylanase 10B from T. maritima MSB8 has been crystallized. A complete diffraction data set was collected up to 2.5  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1662-1664  [ doi:10.1107/S0907444903015464 ]

Crystallization and preliminary X-ray analysis of inorganic polyphosphate/ATP-glucomannokinase from Arthrobacter sp. strain KM

T. Mukai, S. Kawai, S. Mori, B. Mikami and K. Murata

Synopsis: The crystallization of and preliminary X-ray data for inorganic polyphosphate [poly(P)]/ATP-glucomannokinase from Arthrobacter sp. strain KM are presented.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1665-1667  [ doi:10.1107/S0907444903015452 ]

Purification, crystallization and preliminary diffraction studies of the Pseudomonas aeruginosa strain K122-4 monomeric pilin

G. F. Audette, R. T. Irvin and B. Hazes

Synopsis: The expression, purification, crystallization and preliminary X-ray diffraction studies of the monomeric pilin from P. aeruginosa strain K122-4 are reported.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1668-1669  [ doi:10.1107/S0907444903015476 ]

Crystallization and preliminary X-ray diffraction studies on recombinant diaminopropionate ammonia lyase from Escherichia coli

V. Rajaram, J. Rajaganapathi, F. Khan, H. S. Savithri and M. R. N. Murthy

Synopsis: The PLP-dependent enzyme diaminopropionate ammonia lyase from E. coli has been crystallized in two forms. The monoclinic (P2₁) and the tetragonal (P4₁2₁2 or P4₃2₁2) forms diffracted X-rays to 2.5 and 3.0  Å resolution, respectively.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1670-1673  [ doi:10.1107/S0907444903014094 ]

Preliminary X-ray characterization and phasing of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus

I. Noach, R. Lamed, Q. Xu, S. Rosenheck, L. J. W. Shimon, E. A. Bayer and F. Frolow

Synopsis: Native and SeMet derivatives of a type II cohesin from the cellulosomal system of A. cellulolyticus have been expressed, purified and crystallized in a trigonal form. Diffraction data were collected to 1.90  Å. In addition, orthorhombic crystals of the native protein were obtained that diffracted to 1.2  Å. Structures were solved using a combination of SIRAS and molecular replacement.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1674-1675  [ doi:10.1107/S0907444903015816 ]

Crystallization and preliminary crystallographic studies of Escherichia coli CcmG/DsbE protein

N. Ouyang, W.-Y. Chen, Q. Li, Y.-G. Gao, H.-Y. Hu and Z.-X. Xia

Synopsis: E. coli CcmG/DsbE has been crystallized using the vapour-diffusion technique and X-ray data have been collected to 1.9  Å resolution.

Online 19 August 2003

 

Acta Cryst. (2003). D59, 1676-1678  [ doi:10.1107/S0907444903014306 ]

Structure and oligomeric state of the mammalian tumour-associated antigen UK114

D. Deriu, C. Briand, E. Mistiniene, V. Naktinis and M. G. Grütter

Synopsis: The crystal structure of UK114 has been determined, revealing a trimeric arrangement. It was confirmed by ultracentrifugation studies that UK114 is also a trimer in solution.

PDB reference: 1nq3

Online 19 August 2003