Acta Crystallographica Section D

Biological Crystallography

Volume 61, Part 7 (July 2005)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The structure of air-oxidized P. abyssi rubredoxin mutant W4L/R5S solved by direct methods and refined by partially restrained full-matrix least-squares refinement to 0.69 Å resolution (p. 990).

obituaries


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Acta Cryst. (2005). D61, 845-849  [ doi:10.1107/S0907444905014964 ]

M. Sundaralingam (1931-2004): distinguished nucleic acid researcher

N. Yathindra

Synopsis: Obituary for M. Sundaralingam.

Online 24 June 2005


research papers


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Acta Cryst. (2005). D61, 850-855  [ doi:10.1107/S0907444905007894 ]

A robust bulk-solvent correction and anisotropic scaling procedure

P. V. Afonine, R. W. Grosse-Kunstleve and P. D. Adams

Synopsis: A robust method for determining bulk-solvent and anisotropic scaling parameters for macromolecular refinement is described. A maximum-likelihood target function for determination of flat bulk-solvent model parameters and overall anisotropic scale factor is also proposed.

Online 24 June 2005


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Acta Cryst. (2005). D61, 856-862  [ doi:10.1107/S0907444905005421 ]

Structure of human PNP complexed with ligands

F. Canduri, R. G. Silva, D. M. dos Santos, M. S. Palma, L. A. Basso, D. S. Santos and W. F. de Azevedo

Synopsis: This work reports the structure of human PNP in complex with guanosine (at 2.80 Å resolution), 3'-deoxyguanosine (at 2.86 Å resolution) and 8-azaguanine (at 2.85 Å resolution). These structures were compared with the PNP-guanine, PNP-inosine and PNP-immucillin-H complexes solved previously.

PDB references: 1rfg, 1v45 and 1v41

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 863-872  [ doi:10.1107/S0907444905007882 ]

Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines

W. Bu, E. C. Settembre, M. H. el Kouni and S. E. Ealick

Synopsis: The structures of uridine phosphorylase complexed with several acyclic nucleoside analog inhibitors have been determined.

PDB references: 1u1c, 1u1d, 1u1e, 1u1f and 1u1g

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 873-880  [ doi:10.1107/S0907444905007948 ]

Evaluation of protein crystallization states based on texture information derived from greyscale images

K. Saitoh, K. Kawabata, H. Asama, T. Mishima, M. Sugahara and M. Miyano

Synopsis: The method presented here evaluates protein crystallization states automatically.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 881-890  [ doi:10.1107/S090744490500836X ]

High-pressure cooling of protein crystals without cryoprotectants

C. U. Kim, R. Kapfer and S. M. Gruner

Synopsis: Protein crystals were successfully cryocooled by a He-gas high-pressure cooling method without any penetrative cryoprotectants. Excellent diffraction was observed. This method eliminates the need for penetrative cryoprotectants, thereby facilitating crystallographic data collection.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 891-898  [ doi:10.1107/S0907444905008541 ]

The temperature of flash-cooling has dramatic effects on the diffraction quality of nucleosome crystals

R. S. Edayathumangalam and K. Luger

Synopsis: Small changes in temperatures during flash-cooling have significant effects on the diffraction quality of nucleosome crystals and in some cases cause substantial changes in unit-cell parameters that are a result of the reorganization of molecules in the lattice. Thus, in cases where flash-cooling around liquid-nitrogen temperatures leads to a deterioration in diffraction, flash-cooling at intermediate temperatures using alternative cryogens may be a useful approach.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 899-902  [ doi:10.1107/S0907444905008553 ]

Improving experimental phasing: the role of strongest reflections

Y. Vekhter

Synopsis: Analysis shows that merging isomorphous replacement data with a limited number of highly accurate phases from the reference-beam diffraction experiment would significantly improve conventional experimental phasing.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 903-912  [ doi:10.1107/S0907444905008723 ]

Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif

Y. A. Leduc, L. Prasad, M. Laivenieks, J. G. Zeikus and L. T. J. Delbaere

Synopsis: The crystal structure of PEP carboxykinase from a succinate-producing bacterium has been solved in the native form and in complex with pyruvate, manganese and phosphate. The structure of the complex reveals 2-mercaptoethanol covalently bound to a cysteine residue located within a previously unreported conserved motif in the active-site cleft. This motif also contains an important interdomain connection.

PDB references: 1ygg and 1ylh

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 913-919  [ doi:10.1107/S0907444905008838 ]

Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus

P. H. Rehse, T. Kitao and T. H. Tahirov

Synopsis: Apo and cofactor-bound structures of T. thermophilus uroporphyrinogen-III C-methyltransferase solved to 2.0 Å resolution. These structures represent the `closed' form of the protein.

PDB references: 1va0 and 1v9a

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 920-931  [ doi:10.1107/S0907444905009042 ]

Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase

H.-K. Kim, J.-W. Liu, P. D. Carr and D. L. Ollis

Synopsis: In vitro directed evolution of this enzyme produced mutants with enhanced activity towards a non-physiological substrate. X-ray crystallography was used to follow the resulting structural changes and explain the mechanistic implications.

PDB references: 1zi6, 1zic, 1zi9, 1zi8, 1zix, 1ziy, 1zj4 and 1zj5

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 932-941  [ doi:10.1107/S0907444905009546 ]

Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects

J. Wang, S.-H. Rho, H. H. Park and S. H. Eom

Synopsis: An incorrect HslV-HslU quaternary structure can result from two biologically functional complexes sitting at the interface of two coherently associated lattices.

PDB reference: 1yyf

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 942-950  [ doi:10.1107/S0907444905009601 ]

Structure of insect-cell-derived IL-22

T. Xu, N. J. Logsdon and M. R. Walter

Synopsis: The crystal structure of glycosylated interleukin-22 has been determined at 2.6 Å resolution. The structure provides new insights into IL-22 receptor recognition.

PDB reference: 1ykb

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 951-959  [ doi:10.1107/S0907444905010541 ]

SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination

Z.-Q. Fu, J. Rose and B.-C. Wang

Synopsis: A method and a software suite based on it are described for searching both program and parameter space to find the best solution for a given X-ray diffraction data set of protein crystals.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 960-966  [ doi:10.1107/S0907444905010644 ]

Away from the edge II: in-house Se-SAS phasing with chromium radiation

H. Xu, C. Yang, L. Chen, I. A. Kataeva, W. Tempel, D. Lee, J. E. Habel, D. Nguyen, J. W. Pflugrath, J. D. Ferrara, W. B. Arendall, J. S. Richardson, D. C. Richardson, Z.-J. Liu, M. G. Newton, J. P. Rose and B.-C. Wang

Synopsis: High-throughput de novo structure solution and refinement based on a single data set collected with chromium K[alpha] radiation is described.

PDB reference: 1xho

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 967-975  [ doi:10.1107/S0907444905011285 ]

Pathological crystallography: case studies of several unusual macromolecular crystals

Z. Dauter, I. Botos, N. LaRonde-LeBlanc and A. Wlodawer

Synopsis: Structures of several proteins were solved from crystals that exhibited phenomena such as the simultaneous presence of two lattice types, pseudosymmetry accompanied by twinning and unusual types of non-isomorphism.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 976-981  [ doi:10.1107/S0907444905011558 ]

Optimizing statistical Shake-and-Bake for Se-atom substructure determination

H. Xu, C. M. Weeks and H. A. Hauptman

Synopsis: The statistical Shake-and-Bake procedure is optimized for Se-atom substructure determination.

Online 24 June 2005


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Acta Cryst. (2005). D61, 982-989  [ doi:10.1107/S0907444905012746 ]

The effects of flash-annealing on glycerol kinase crystals

A. Vahedi-Faridi, V. Stojanoff and J. I. Yeh

Synopsis: The reflection profiles from glycerol kinase crystals were analyzed using highly monochromatic parallel synchrotron radiation and fine [varphi]-slicing to elucidate the effects of flash-cooling on diffraction quality.

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 990-1004  [ doi:10.1107/S090744490501293X ]

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 Å X-ray structure of mutant W4L/R5S

H. Bönisch, C. L. Schmidt, P. Bianco and R. Ladenstein

Synopsis: The structure of air-oxidized P. abyssi rubredoxin mutant W4L/R5S was solved by direct methods and refined by partially restrained full-matrix least-squares refinement to 0.69 Å resolution.

PDB references: 1yk4 and 1yk5

Online 24 June 2005


short communications


 

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Acta Cryst. (2005). D61, 1005-1008  [ doi:10.1107/S0907444905009364 ]

Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols

A. Deshpande, S. Nimsadkar and S. C. Mande

Synopsis: The effect of alcohols on protein structure has been studied by crystallography. Increasing solvent hydrophobicity is seen to be proportional to the overall dehydration of a protein's water shell.

PDB references: 1z55, 1ykx, 1yky, 1ykz, 1yl0 and 1yl1

Online 24 June 2005


 

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Acta Cryst. (2005). D61, 1009-1012  [ doi:10.1107/S0907444905015404 ]

The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs

A. Canals, M. Purciolas, J. Aymamí and M. Coll

Synopsis: The 1.5 Å resolution crystallographic structure of a 6 bp DNA in complex with ellipticine confirms the intercalative binding previously described in a self-complementary ribodinucleoside monophosphate and enables an accurate measurement of the distortion effects of the drug on real DNA.

PDB reference: 1z3f

Online 24 June 2005


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