Acta Crystallographica Section D

Biological Crystallography

Volume 60, Part 6 (June 2004)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Hexameric assembly of E. coli MoaB viewed along the threefold crystallographic symmetry axis (p. 1068).

research papers


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Acta Cryst. (2004). D60, 987-998  [ doi:10.1107/S0907444904005268 ]

Accurate rocking-curve measurements on protein crystals grown in a homogeneous magnetic field of 2.4 T

D. Lübbert, A. Meents and E. Weckert

Synopsis: The anisotropic mosaicity of protein crystals was investigated using high-resolution X-ray diffraction rocking-curve measurements. Statistical data analysis was used to quantitatively evaluate whether a homogeneous magnetic field of 2.4 T applied during crystal growth can lead to improved crystal quality in the example of the tetragonal form of hen egg-white lysozyme.

Online 21 May 2004


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Acta Cryst. (2004). D60, 999-1007  [ doi:10.1107/S090744490400602X ]

Azospirillum irakense pectate lyase displays a toroidal fold

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

Synopsis: The crystal structure of A. irakense pectate lyase (PelA) has been determined at a resolution of 2.65 Å. The overall structure of PelA does not adopt the characteristic parallel [beta]-helix fold displayed by pathogenic pectate lyases; instead, it displays a predominantly [alpha]-helical structure with irregular coils and short [beta]-strands.

PDB reference: 1r76

Online 21 May 2004


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Acta Cryst. (2004). D60, 1008-1016  [ doi:10.1107/S090744490400616X ]

Short hydrogen bonds in photoactive yellow protein

S. Anderson, S. Crosson and K. Moffat

Synopsis: Photoactive yellow protein was solved at high resolution under a variety of conditions in order to investigate the unusually short hydrogen bonds to its coumaric acid chromophore.

PDB references: 1otb, 1ota, 1ot9, 1ot6, 1oti, 1ote and 1otd

Online 21 May 2004


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Acta Cryst. (2004). D60, 1017-1023  [ doi:10.1107/S0907444904006225 ]

A benzoic acid inhibitor induces a novel conformational change in the active site of Influenza B virus neuraminidase

B. S. Lommer, S. M. Ali, S. N. Bajpai, W. J. Brouillette, G. M. Air and M. Luo

Synopsis: A novel benzoic acid inhibitor of influenza virus neuraminidase induces a previously unobserved conformational change in the side chain of the crucial active-site residue Glu275.

PDB reference: 1vcj

Online 21 May 2004


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Acta Cryst. (2004). D60, 1024-1031  [ doi:10.1107/S0907444904006377 ]

Phasing in the presence of severe site-specific radiation damage through dose-dependent modelling of heavy atoms

M. Schiltz, P. Dumas, E. Ennifar, C. Flensburg, W. Paciorek, C. Vonrhein and G. Bricogne

Synopsis: It is shown that in the presence of severe site-specific radiation damage the use of unmerged data and a parametrization that implements dose-dependent occupancies for the anomalous scatterers can give significant improvements in SAD/MAD and/or heavy-atom phases. Such an option is now implemented in the program SHARP; results on a brominated RNA molecule are presented.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1032-1039  [ doi:10.1107/S0907444904006559 ]

More rapid evaluation of biomacromolecular crystals for diffraction experiments

S. Arai, T. Chatake, N. Suzuki, H. Mizuno and N. Niimura

Synopsis: The crystal quality of three kinds of biomolecules have been assessed by a `relative Wilson plot' method and a rational method has been developed for estimating crystal quality.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1040-1047  [ doi:10.1107/S0907444904006948 ]

Structural determination of a partially hemihedrally twinned actin crystal

L. Govindasamy, R. Reutzel, M. Agbandje-McKenna and R. McKenna

Synopsis: An orthorhombic actin crystal was converted into a partially hemihedrally twinned tetragonal crystal by condensation induced by flash-freezing. The structure, with two actin molecules in the crystallographic asymmetric unit, was determined by molecular-replacement methods.

PDB reference: 1rfq

Online 21 May 2004


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Acta Cryst. (2004). D60, 1048-1056  [ doi:10.1107/S0907444904007000 ]

Structure of concanavalin A at pH 8: bound solvent and crystal contacts

F. J. López-Jaramillo, L. A. González-Ramírez, A. Albert, F. Santoyo-González, A. Vargas-Berenguel and F. Otálora

Synopsis: The crystal structure of Mn-Mn ConA grown by the gel-acupuncture method at pH 8 contains 25 molecules of glycerol, the majority of them at conserved positions. A relation exists between the crystal contacts and the space group, the contact Asp58-Ser62 being a universal feature of ConA crystals.

PDB reference: 1nxd

Online 21 May 2004


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Acta Cryst. (2004). D60, 1057-1067  [ doi:10.1107/S090744490400695X ]

A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry

R. H. Lilien, C. Bailey-Kellogg, A. C. Anderson and B. R. Donald

Synopsis: This paper presents an efficient quaternion-based algorithm for analyzing peaks from a cross-rotation function to identify model orientations consistent with proper non-crystallographic symmetry (NCS), and to generate NCS-consistent orientations missing from the list of cross-rotation peaks.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1068-1075  [ doi:10.1107/S0907444904007164 ]

Structure of the molybdenum-cofactor biosynthesis protein MoaB of Escherichia coli

G. Bader, M. Gomez-Ortiz, C. Haussmann, A. Bacher, R. Huber and M. Fischer

Synopsis: The crystal structure of E. coli MoaB protein and a detailed comparison with the homologues MogA, Cnx1 G-domain and gephyrin are reported.

PDB reference: 1r2k

Online 21 May 2004


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Acta Cryst. (2004). D60, 1076-1084  [ doi:10.1107/S0907444904007437 ]

The role of CAPS buffer in expanding the crystallization space of the nucleotide-binding domain of the ABC transporter haemolysin B from Escherichia coli

J. Zaitseva, I. B. Holland and L. Schmitt

Synopsis: A simple screening test for optimized stabilization and conditions for an ABC-ATPase was established that preserves activity, avoids precipitation and provided material suitable for crystallization and X-ray analysis for all of the functional states of the catalytic cycles of the HlyB-NBD.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1085-1093  [ doi:10.1107/S0907444904007917 ]

Structural effects of radiation damage and its potential for phasing

S. Banumathi, P. H. Zwart, U. A. Ramagopal, M. Dauter and Z. Dauter

Synopsis: An analysis of radiation-damage-induced structural and intensity changes is presented on the model protein thaumatin.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1094-1100  [ doi:10.1107/S0907444904008522 ]

Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii

H. Itou, M. Yao, N. Watanabe and I. Tanaka

Synopsis: The crystal structure of PH1161 protein, a transcriptional activator B. subtilis TenA homologue from P. horikoshii, was analyzed at 2.15 Å resolution.

PDB reference: 1udd

Online 21 May 2004


structural genomics papers


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Acta Cryst. (2004). D60, 1101-1107  [ doi:10.1107/S0907444904007188 ]

Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 Å resolution

I. Janda, Y. Devedjiev, D. Cooper, M. Chruszcz, U. Derewenda, A. Gabrys, W. Minor, A. Joachimiak and Z. S. Derewenda

Synopsis: This paper reports the crystal structure of the product of the YdeN gene.

PDB reference: 1uxo

Online 21 May 2004


crystallization papers


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Acta Cryst. (2004). D60, 1108-1111  [ doi:10.1107/S0907444904005670 ]

Purification, partial characterization, crystallization and preliminary X-ray diffraction of two cysteine-rich secretory proteins from Naja atra and Trimeresurus stejnegeri venoms

J. Wang, M. Guo, X. Tu, D. Zheng, M. Teng, L. Niu, Q. Liu, Q. Huang and Q. Hao

Synopsis: The purification and crystallization of two cysteine-rich secretory protein (CRISP) family members, natrin and stecrisp from N. atra and T. stejnegeri venoms, allowed the collection of two complete data sets to 2.1 and 1.6 Å resolution, respectively.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1112-1114  [ doi:10.1107/S090744490400678X ]

Crystallization and preliminary crystallographic analysis of SMase I, a sphingomyelinase from Loxosceles laeta spider venom

S. P. Zela, M. F. Fernandes Pedrosa, M. T. Murakami, S. A. de Andrade, R. K. Arni and D. V. Tambourgi

Synopsis: L. laeta SMase I, a 32 kDa sphingomyelinase present in L. laeta venom, has been crystallized and diffraction data have been collected to 1.8 Å resolution.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1115-1117  [ doi:10.1107/S0907444904006961 ]

Crystallization and preliminary X-ray crystallographic analysis of the DNA-binding domain of BldD from Streptomyces coelicolor A3(2)

I.-K. Kim, M.-K. Kim, C.-J. Lee, H.-S. Yim, S.-S. Cha and S.-O. Kang

Synopsis: The DNA-binding domain of BldD from S. coelicolor has been crystallized. The crystals diffract to 1.8 Å resolution and belong to space group C2.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1118-1120  [ doi:10.1107/S090744490400705X ]

Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis

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

Synopsis: Nogalonic acid methyl ester cyclase, a polyketide cyclase in the biosynthetic pathway of the antibiotic nogalamycin, has been crystallized. The crystals obtained in the presence of the substrate are orthorhombic, space group I222, with unit-cell parameters a = 69.1, b = 72.0, c = 65.4 Å and diffract to 1.35 Å resolution.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1121-1124  [ doi:10.1107/S0907444904007395 ]

Purification, characterization and preliminary crystallographic studies of a novel plant defensin from Pachyrrhizus erosus seeds

X. Song, Z. Zhou, J. Wang, F. Wu and W. Gong

Synopsis: A novel plant defensin protein, SPE10, was isolated and characterized from P. erosus seeds. Preliminary crystallographic studies have been performed.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1125-1128  [ doi:10.1107/S0907444904007577 ]

Expression, purification and crystallization of two peroxisomal acyl-CoA oxidases from Arabidopsis thaliana

L. Pedersen and A. Henriksen

Synopsis: Two peroxisomal acyl-CoA oxidase enzymes from A. thaliana have been expressed in E. coli and one of them was crystallized in a selenomethionine-substituted form. Diffraction data from both enzymes have been collected at synchrotron sources.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1129-1131  [ doi:10.1107/S090744490400767X ]

Overexpression, purification and crystallization of PhzA, the first enzyme of the phenazine biosynthesis pathway of Pseudomonas fluorescens 2-79

E. G. Ahuja, D. V. Mavrodi, L. S. Thomashow and W. Blankenfeldt

Synopsis: The cloning, overexpression and crystallization of PhzA, an enzyme involved in the final steps of phenazine-1-carboxylic acid biosynthesis, were undertaken. Details of data collection from both native and seleno-L-methionine-labelled crystals are described.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1132-1134  [ doi:10.1107/S0907444904007814 ]

Crystallization of CcdB in complex with a GyrA fragment

M.-H. Dao-Thi, L. Van Melderen, E. De Genst, L. Buts, A. Ranquin, L. Wyns and R. Loris

Synopsis: GyrA14, a fragment of GyrA, was crystallized in its free state and as a complex with the toxin CcdB.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1135-1136  [ doi:10.1107/S0907444904007735 ]

Cloning, purification, crystallization and preliminary crystallographic analysis of acylphosphatase from Pyrococcus horikoshii OT3

K. Miyazono, N. Kudo and M. Tanokura

Synopsis: Acylphosphatase from a hyperthermophilic archaea, P. horikoshii OT3, has been crystallized and X-ray diffraction data have been collected to 1.72 Å resolution.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1137-1138  [ doi:10.1107/S0907444904007905 ]

Expression, purification and preliminary X-ray diffraction analysis of a ketoreductase from a type II polyketide synthase

W. Teartasin, C. Limpkin, F. Glod, J. Spencer, R. J. Cox, T. J. Simpson, J. Crosby, M. P. Crump and A. T. Hadfield

Synopsis: The S. coelicolor actIII ORF5 gene has been isolated and cloned into a His-tagged vector to overexpress an active NADPH-dependent ketoreductase used in type II polyketide synthesis. Protein crystals obtained in the presence of NADP+ diffract to 2.5 Å.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1139-1141  [ doi:10.1107/S0907444904007991 ]

Crystallization and preliminary crystallographic analysis of a novel haemolytic lectin from the mushroom Laetiporus sulphureus

J. M. Mancheño, H. Tateno, I. J. Goldstein and J. A. Hermoso

Synopsis: A novel haemolytic lectin from the parasitic mushroom L. sulphureus has been crystallized by the hanging-drop vapour-diffusion method. Native data have been collected to 2.7 Å resolution.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1142-1144  [ doi:10.1107/S0907444904007929 ]

Overproduction, crystallization and preliminary crystallographic analysis of a novel human DNA-repair enzyme that recognizes oxidative DNA damage

V. Bandaru, W. Cooper, S. S. Wallace and S. Doublié

Synopsis: The expression, purification, crystallization and preliminary X-ray analysis of a novel human DNA glycosylase are presented.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1145-1148  [ doi:10.1107/S0907444904008078 ]

Crystallization and preliminary crystallographic analysis of an Enterococcus faecalis repressor protein, CylR2, involved in regulating cytolysin production through quorum-sensing

S. Ni, K. McAteer, D. E. Bussiere and M. A. Kennedy

Synopsis: CylR2 was expressed with a C-terminal six-histidine tag and purified to homogeneity with a cobalt-affinity column followed by size-exclusion chromatography. Both native and SeMet proteins were produced and crystallized.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1149-1151  [ doi:10.1107/S0907444904008534 ]

Crystallization and preliminary X-ray diffraction analysis of a thermostable endo-1,5-[alpha]-L-arabinanase from Bacillus thermodenitrificans TS-3

A. Yamaguchi, T. Tada, T. Nakaniwa, T. Kitatani, M. Takao, T. Sakai and K. Nishimura

Synopsis: The thermostable endo-1,5-[alpha]-L-arabinanase ABN-TS from B. thermodenitrificans TS-3 was crystallized. A complete diffraction data set was collected to 1.9 Å resolution using synchrotron radiation.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1152-1154  [ doi:10.1107/S0907444904008558 ]

Crystallization and preliminary crystallographic analysis of Bacillus subtilis guanine deaminase

Y.-J. Chang, C.-H. Huang, C.-Y. Hu and S.-H. Liaw

Synopsis: Crystallization of B. subtilis guanine deaminase, a key enzyme in nucleotide metabolism which catalyzes the hydrolytic deamination of guanine to xanthine.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1155-1157  [ doi:10.1107/S090744490400873X ]

Cloning, expression, purification, crystallization and preliminary crystallographic analysis of [gamma]-filamin repeat 23

Lj. Sjekloca, B. Sjöblom, M. Polentarutti and K. Djinovic Carugo

Synopsis: [gamma]-Filamin is a multidomain protein present in the myofibrillar Z-disc, where it cross-links the actin filaments. Recombinant repeat 23 of [gamma]-filamin was crystallized and a SAD data set was collected to 2.05 Å resolution.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1158-1160  [ doi:10.1107/S0907444904009564 ]

Crystallization and preliminary crystallographic analysis of the motor domain of human kinetochore-associated protein CENP-E using an automated crystallization procedure

I. Garcia-Saez, D. Blot, R. Kahn and F. Kozielski

Synopsis: Crystals of the motor domain of the human centromere-associated protein E (CENP-E) have been obtained by high-throughput crystallization screening using an automated TECAN crystallization robot. The best-diffracting crystals belong to space group P21, with unit-cell parameters a = 49.35, b = 83.70, c = 94.16 Å, [beta] = 103.05°, and diffract to better than 2.1 Å.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1161-1164  [ doi:10.1107/S0907444904009515 ]

Crystallization and preliminary crystallographic analysis of the fusion core from two new zoonotic paramyxoviruses, Nipah virus and Hendra virus

Y. Xu, Z. Lou, Y. Liu, D. K. Cole, N. Su, L. Qin, X. Li, Z. Bai, Z. Rao and G. F. Gao

Synopsis: Crystals of the fusion core of both Nipah and Hendra viruses were obtained; the crystals diffract X-rays to 2.0-2.1 Å.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1165-1166  [ doi:10.1107/S0907444904009412 ]

Crystallization and preliminary X-ray crystallographic analyses of EcoO109I and its complex with DNA

T. Imasaki, H. Hashimoto, T. Shimizu, M. Kato, J. Tsuda, K. Kita and M. Sato

Synopsis: Tetragonal and orthorhombic crystals of EcoO109I and its complex with DNA were obtained and diffraction data were collected to 2.4 and 1.9 Å resolution, respectively.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1167-1169  [ doi:10.1107/S0907444904009783 ]

Crystallization and preliminary X-ray analysis of [alpha]-isopropylmalate synthase from Mycobacterium tuberculosis

N. Koon, C. J. Squire and E. N. Baker

Synopsis: [alpha]-Isopropylmalate synthase from M. tuberculosis (Rv3710), which catalyses the first committed step of leucine biosynthesis, has been expressed, purified and crystallized in a form suitable for high-resolution X-ray structural analysis.

Online 21 May 2004


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Acta Cryst. (2004). D60, 1170-1172  [ doi:10.1107/S0907444904009928 ]

Purification and crystallization of the heterodimeric complex of RAR[beta] and RXR[alpha] ligand-binding domains in the active conformation

V. Pogenberg, J.-F. Guichou and W. Bourguet

Synopsis: This study describes the crystallization and preliminary X-ray analysis of a heterodimer containing the ligand-binding domains of the retinoid X receptor [alpha] and of the retinoic acid receptor [beta] in complex with 9-cis-retinoic acid and a fragment of the transcriptional coactivator TRAP220. The complex crystallizes in space group P3121 and diffracts to 2.9 Å resolution.

Online 21 May 2004


short communications


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Acta Cryst. (2004). D60, 1173-1176  [ doi:10.1107/S0907444904003403 ]

Structure of the isoaspartyl peptidase with L-asparaginase activity from Escherichia coli

A. Prahl, M. Pazgier, M. Hejazi, W. Lockau and J. Lubkowski

Synopsis: The crystal structure of the plant-type asparaginase from E. coli, EcAIII, has been solved by molecular replacement and refined to a resolution of 1.65 Å. Sodium ion-binding sites have been identified that were not observed in other related enzymes. The structure of EcAIII helps to explain some of the differences between the substrate specificities of plant-type asparaginases and glycosylasparaginases.

PDB reference: 1t3m

Online 21 May 2004


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Acta Cryst. (2004). D60, 1177-1179  [ doi:10.1107/S0907444904006808 ]

Three-dimensional structural characterization of a novel Drosophila melanogaster acylphosphatase

S. Zuccotti, C. Rosano, M. Ramazzotti, D. Degl'Innocenti, M. Stefani, G. Manao and M. Bolognesi

Synopsis: The crystal structure of a novel acylphosphatase (AcpDro2) has been solved at 1.5 Å resolution in order to improve knowledge of the enzyme catalytic cycle as well as of the molecular basis of protein folding, misfolding and aggregation.

PDB reference: 1urr

Online 21 May 2004


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Acta Cryst. (2004). D60, 1180-1184  [ doi:10.1107/S0907444904007334 ]

The structure of a triple mutant of pI258 arsenate reductase from Staphylococcus aureus and its 5-thio-2-nitrobenzoic acid adduct

J. Messens, I. Van Molle, P. Vanhaesebrouck, K. Van Belle, K. Wahni, J. C. Martins, L. Wyns and R. Loris

Synopsis: The ArsC triple mutant C10SC15AC82S has a structure that is very similar to that of the reduced form of wild-type ArsC, with a folded redox helix and a buried catalytic Cys89. In the adduct form, the TNB molecule is buried in a hydrophobic pocket and the disulfide bridge between TNB and Cys89 is sterically inaccessible to thioredoxin.

PDB references: 1rxi and 1rxe

Online 21 May 2004


addenda and errata


 

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Acta Cryst. (2004). D60, 1185  [ doi:10.1107/S0907444904007838 ]

Characterization, crystallization and preliminary X-ray analysis of bifunctional dihydrofolate reductase-thymidylate synthase from Plasmodium falciparum. Erratum

P. Chitnumsub, J. Yuvaniyama, J. Vanichtanankul, S. Kamchonwongpaisan, M. D. Walkinshaw and Y. Yuthavong

Synopsis: An erratum to the paper by Chitnumsub et al. (2004), Acta Cryst. D60, 780-783.

Online 21 May 2004


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