Acta Crystallographica Section D

Biological Crystallography

Volume 58, Part 5 (May 2002)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The different packing patterns of three crystal forms of S. typhi 3-dehydroquinase (p. 798).

research papers


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Acta Cryst. (2002). D58, 727-734  [ doi:10.1107/S0907444902002652 ]

3-Carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenomethionines

M. C. Merckel, T. Kajander, A. M. Deacon, A. Thompson, J. G. Grossmann, N. Kalkkinen and A. Goldman

Synopsis: The structure determination of 3-carboxy-cis,cis-muconate lactonizing enzyme from N. crassa by MAD at 3.0 Å is described and some of the difficulties in the structure determination and the methods used to address them are discussed. This represents one of the largest selenium substructures (80 Se atoms) solved.

PDB reference: 1jof

Online 26 April 2002


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Acta Cryst. (2002). D58, 735-743  [ doi:10.1107/S0907444901019588 ]

Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibility

K. A. Kantardjieff, P. Höchtl, B. W. Segelke, F.-M. Tao and B. Rupp

Synopsis: A new structure of concanavalin A, in a dimeric crystal form, has been refined using effective model-bias removal methods. The structure provides an opportunity to examine model accuracy and coordinate precision in high- or atomic resolution protein structures.

PDB reference: 1gkb

Online 26 April 2002


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Acta Cryst. (2002). D58, 744-750  [ doi:10.1107/S0907444902003207 ]

The structure of substrate-free microbial ribonuclease binase and of its complexes with 3'GMP and sulfate ions

K. M. Polyakov, A. A. Lebedev, A. L. Okorokov, K. I. Panov, A. A. Schulga, A. G. Pavlovsky, M. Ya. Karpeisky and G. G. Dodson

Synopsis: The structure of binase, a member of the guanyl-specific microbial ribonuclease family of proteins, has been solved as a free enzyme at 1.65 Å resolution. This structure is compared with the binase complexes with 3'GMP and sulfate ions determined with data extending to 2.0 Å resolution.

PDB references: 1gou, 1gov and 1goy

Online 26 April 2002


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Acta Cryst. (2002). D58, 751-760  [ doi:10.1107/S0907444902002767 ]

Thaumatin crystallization aboard the International Space Station using liquid-liquid diffusion in the Enhanced Gaseous Nitrogen Dewar (EGN)

C. L. Barnes, E. H. Snell and C. E. Kundrot

Synopsis: The first biological crystal-growth experiment on the International Space Station used the Enhanced Gaseous Nitrogen Dewar and produced thaumatin crystals diffracting to 1.28 Å, which is comparable to previous space-grown thaumatin crystals and better than the best ground-control crystal (1.47 Å).

Online 26 April 2002


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Acta Cryst. (2002). D58, 761-767  [ doi:10.1107/S0907444902003402 ]

Simulated-annealing real-space refinement as a tool in model building

A. Korostelev, R. Bertram and M. S. Chapman

Synopsis: Real-space simulated-annealing refinement is implemented within an interactive molecular graphics package. This accelerates the rate-limiting step of model building and improves the starting point and final quality of subsequent conventional refinement.

Online 26 April 2002


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Acta Cryst. (2002). D58, 768-776  [ doi:10.1107/S0907444902003359 ]

Conformations of amino acids in proteins

S. Hovmöller, T. Zhou and T. Ohlson

Synopsis: Ramachandran plots for all 20 amino acids were produced from 1042 protein subunits from the PDB, separately for those in SHEET, HELIX and Random coil. The classical Ramachandran plot needs to be revised in every detail. Most amino acids have two distinct conformations in the [beta]-sheet region - one more frequent when the amino acids are really parts of SHEET and the other more typical for those occurring in Random coil. Amino acids in parallel and antiparallel [beta]-strands have nearly the same conformations.

Online 26 April 2002


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Acta Cryst. (2002). D58, 777-783  [ doi:10.1107/S0907444902003724 ]

The mechanism of iron uptake by transferrins: the X-ray structures of the 18 kDa NII domain fragment of duck ovotransferrin and its nitrilotriacetate complex

P. Kuser, D. R. Hall, M. L. Haw, M. Neu, R. W. Evans and P. F. Lindley

Synopsis: The crystal structures of the 18 kDa NII-domain fragment of duck ovotransferrin and its complex with nitrilotriacetate are reported at resolutions of 1.95 and 1.90 Å, respectively. The implication of these structures with respect to the mechanism of iron binding by the transferrins is discussed.

PDB references: 1gv8 and 1gvc

Online 26 April 2002


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Acta Cryst. (2002). D58, 784-791  [ doi:10.1107/S090744490200392X ]

Detection and characterization of merohedral twinning in two protein crystals: bacteriorhodopsin and p67phox

A. Royant, S. Grizot, R. Kahn, H. Belrhali, F. Fieschi, E. M. Landau and E. Pebay-Peyroula

Synopsis: A combination of various approaches was used to determine precise twinning ratios. The importance of second-, third-, and fourth-order moments is discussed.

Online 26 April 2002


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Acta Cryst. (2002). D58, 792-797  [ doi:10.1107/S0907444902003931 ]

Rearrangement of Cruickshank's formulae for the diffraction-component precision index

D. M. Blow

Synopsis: Formulae for the diffraction-component precision index are rearranged for easy calculation and to show how precision varies with such quantities as resolution and completeness of observation.

Online 26 April 2002


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Acta Cryst. (2002). D58, 798-804  [ doi:10.1107/S0907444902003918 ]

Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity

W.-H. Lee, L. A. Perles, R. A. P. Nagem, A. K. Shrive, A. Hawkins, L. Sawyer and I. Polikarpov

Synopsis: Crystal structures of two new crystal forms of the type I 3-dehydroquinate dehydratase (DHQase) have been determined and analysed.

PDB reference: 1l9w

Online 26 April 2002


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Acta Cryst. (2002). D58, 805-814  [ doi:10.1107/S0907444902003943 ]

FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments

M. Roth, P. Carpentier, O. Kaïkati, J. Joly, P. Charrault, M. Pirocchi, R. Kahn, E. Fanchon, L. Jacquamet, F. Borel, A. Bertoni, P. Israel-Gouy and J.-L. Ferrer

Synopsis: FIP is a French CRG beamline at the European Synchrotron Radiation Facility (ESRF) dedicated exclusively to crystallography of biological macromolecules, with a special emphasis on automated multiwavelength anomalous diffraction data collection in the 0.7-1.81 Å wavelength range.

Online 26 April 2002


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Acta Cryst. (2002). D58, 815-823  [ doi:10.1107/S0907444902004183 ]

Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties

P. C. Bourne, P. A. Ramsland, L. Shan, Z.-C. Fan, C. R. DeWitt, B. B. Shultz, S. S. Terzyan, C. R. Moomaw, C. A. Slaughter, L. W. Guddat and A. B. Edmundson

Synopsis: The three-dimensional structure of a human light-chain dimer (Sea) is reported to 1.94 Å resolution. This structure is likely to facilitate our understanding of why some seemingly harmless light chains display a propensity to aggregate as pathological amyloid fibrils.

PDB reference: 1jvk

Online 26 April 2002


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Acta Cryst. (2002). D58, 824-832  [ doi:10.1107/S0907444902004614 ]

The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging

M. Kroemer and G. E. Schulz

Synopsis: The C4-tetrameric enzyme crystallized with 20 protomers in the asymmetric unit. The atomic cstructure was solved using one heavy-atom derivative at 6 Å resolution and the molecular envelope of a related enzyme.

PDB reference: 1gt7

Online 26 April 2002


crystallization papers


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Acta Cryst. (2002). D58, 833-835  [ doi:10.1107/S0907444902005048 ]

Crystallization and preliminary X-ray analysis of the full-size cubic core of pig 2-oxoglutarate dehydrogenase complex

K. Suzuki, W. Adachi, N. Yamada, M. Tsunoda, K. Koike, M. Koike, T. Sekiguchi and A. Takénaka

Synopsis: The full-length (untruncated) protein dihydrolipoamide succinyltransferase, E2, of OGDC from pig heart, has been crystallized in space group I432, with unit-cell parameter a = 189.9 Å.

Online 26 April 2002


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Acta Cryst. (2002). D58, 836-838  [ doi:10.1107/S0907444902001270 ]

Crystallization and preliminary diffraction studies of the ectodomain of the envelope glycoprotein D from herpes simplex virus 1 alone and in complex with the ectodomain of the human receptor HveA

A. Carfí, H. Gong, H. Lou, S. H. Willis, G. H. Cohen, R. J. Eisenberg and D. C. Wiley

Synopsis: The crystallization of the complex between glycoprotein D (gD) from HSV-1 and the receptor HveA is decribed as well as the preparation of a selenomethionine-substituted gD in insect cells.

Online 26 April 2002


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Acta Cryst. (2002). D58, 839-842  [ doi:10.1107/S0907444902002639 ]

Purification, N-terminal sequencing, crystallization and preliminary X-ray diffraction analysis of atratoxin, a new short-chain [alpha]-neurotoxin from the venom of Naja naja atra

X. Tu, Q. Huang, X. Lou, M. Teng and L. Niu

Synopsis: Single crystals of atratoxin have been grown from drops containing the necessary Cu2+ ions by the conventional hanging-drop vapour-diffusion method.

Online 26 April 2002


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Acta Cryst. (2002). D58, 843-845  [ doi:10.1107/S0907444902003499 ]

Characterization and crystallization of a novel haemoglobinase from pathogenic Escherichia coli

J. R. H. Tame, S. J. M. van Dooren, B. Oudega and B. R. Otto

Synopsis: A novel haemoglobinase from pathogenic E. coli has been crystallized. The crystals diffract to 2.5 Å resolution.

Online 26 April 2002


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Acta Cryst. (2002). D58, 846-848  [ doi:10.1107/S0907444902003736 ]

Cloning, high-level expression, purification and crystallization of peptide deformylase from Leptospira interrogans

Y. Li, S. Ren and W. Gong

Synopsis: Peptide deformylase from the pathogenic bacterium L. interrogans was identified. The enzyme was overexpressed in E. coli in high yield. The purified enzyme was crystallized and X-ray diffraction data were collected to 3 Å resolution.

Online 26 April 2002


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Acta Cryst. (2002). D58, 849-852  [ doi:10.1107/S0907444902003700 ]

Crystallization and preliminary X-ray analysis of human carbonic anhydrase III

D. M. Duda, C. Yoshioka, L. Govindasamy, H. An, C. Tu, D. N. Silverman and R. McKenna

Synopsis: Carbonic anhydrases catalyze the interconversion of carbon dioxide to bicarbonate. Human carbonic anhydrase isozyme III with a C-terminal hexahistidine tag was overexpressed in E. coli, purified and crystallized.

Online 26 April 2002


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Acta Cryst. (2002). D58, 853-855  [ doi:10.1107/S0907444902004201 ]

Crystallization and preliminary X-ray analysis of the hydroperoxidase I C-terminal domain from Escherichia coli

X. Carpena, A. Guarné, J. C. Ferrer, P. M. Alzari, I. Fita and P. C. Loewen

Synopsis: The C-terminal domain of catalase-peroxidase HPI (hydroperoxidase I) from E. coli has been crystallized.

Online 26 April 2002


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Acta Cryst. (2002). D58, 856-858  [ doi:10.1107/S0907444902004791 ]

Crystallization of the functional domain of human thrombopoietin using an antigen-binding fragment derived from neutralizing monoclonal antibody

R. Kuroki, M. Hirose, Y. Kato, M. D. Feese, T. Tamada, H. Shigematsu, H. Watarai, Y. Maeda, T. Tahara, T. Kato and H. Miyazaki

Synopsis: The functional domain of human thrombopoietin was crystallized using a Fab fragment digested from its neutralizing antibody. Preliminary X-ray analysis suggests that each Fab fragment provides a suitable interface for crystallization.

Online 26 April 2002


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Acta Cryst. (2002). D58, 859-860  [ doi:10.1107/S0907444902004808 ]

Purification, crystallization and preliminary X-ray diffraction analysis of yeast regulatory particle non-ATPase subunit 6 (Nas6p)

N. Adachi, B. Padmanabhan, K. Kataoka, K. Kijima, M. Yamaki and M. Horikoshi

Synopsis: The regulatory particle non-ATPase subunit, Nas6p, from S. cerevisiae has been crystallized by the hanging-drop method. A complete diffraction data set using synchrotron radiation was collected to 2.6 Å resolution.

Online 26 April 2002


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Acta Cryst. (2002). D58, 861-863  [ doi:10.1107/S0907444902004833 ]

Crystallization and preliminary X-ray crystallographic analysis of aspartate 1-decarboxylase from Helicobacter pylori

A.-R. Kwon, B. I. Lee, B. W. Han, H. J. Ahn, J. K. Yang, H.-J. Yoon and S. W. Suh

Synopsis: Aspartate 1-decarboxylase (PanD) from H. pylori has been overexpressed and crystallized (space group I422; unit-cell parameters a = b = 81.83, c = 93.78 Å). Diffraction data have been collected to 1.55 Å using synchrotron X-rays.

Online 26 April 2002


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Acta Cryst. (2002). D58, 864-866  [ doi:10.1107/S0907444902004845 ]

Crystallization and preliminary X-ray crystallographic analysis of UDP-N-acetylglucosamine acyltransferase from Helicobacter pylori

B. I. Lee, J. Y. Lee, J. Moon, B. W. Han and S. W. Suh

Synopsis: UDP-N-acetylglucosamine acyltransferase (LpxA) from H. pylori has been overexpressed and crystallized (space group P6322; unit-cell parameters a = b = 90.69, c = 148.20 Å, [alpha] = [beta] = 90, [gamma] = 120°). Diffraction data have been collected to 2.1 Å using synchrotron X-rays.

Online 26 April 2002


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Acta Cryst. (2002). D58, 867-869  [ doi:10.1107/S0907444902005012 ]

Towards the crystal structure of glycerol dehydrogenase from Thermotoga maritima

V. Srinivasan, K. Ma, M. W. W. Adams, M. G. Newton, J. P. Rose and B.-C. Wang

Synopsis: The NAD+-dependent glycerol dehydrogenase from the extremely thermophilic bacterium T. maritima has been crystallized in the presence of glycerol by the hanging-drop vapour-diffusion method using 2-methyl-2,4-pentanediol (MPD) as the precipitating agent.

Online 26 April 2002


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Acta Cryst. (2002). D58, 870-871  [ doi:10.1107/S0907444902005036 ]

Crystallization and preliminary X-ray analysis of recombinant histone HPhA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3

T. Li, X. Ji, F. Sun, R. Gao, S. Cao, Y. Feng and Z. Rao

Synopsis: Crystals of recombinant hyperthermophilic archael histone HPhA were obtained by the hanging-drop vapour-diffusion method. Diffraction data have been collected to 2.3 Å.

Online 26 April 2002


short communications


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Acta Cryst. (2002). D58, 872-874  [ doi:10.1107/S0907444902003712 ]

Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium

M. M. Harding

Synopsis: For sodium and potassium, geometry around the metal ion found in high-resolution protein structures in the Protein Data Bank is compared with that in appropriate small-molecule complexes in the Cambridge Structural Database. Target distances for refinement or for validation are proposed.

Online 26 April 2002


 

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Acta Cryst. (2002). D58, 875-877  [ doi:10.1107/S0907444902004031 ]

Spoilt for choice: protein target selection in a time of plenty

J. Raftery and J. R. Helliwell

Synopsis: Exploiting genomic sequence databases for structural genomics target selection.

Online 26 April 2002


addenda and errata


 

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Acta Cryst. (2002). D58, 878  [ doi:10.1107/S0907444902005759 ]

Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6 Å resolution against experimental MAD phases. Addendum

F. Coste, W. Shepard and C. Zelwer

Synopsis: An addendum to Coste et al. [Acta Cryst. (2002) D58, 431-440].

Online 26 April 2002


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