Biological Crystallography

 

Acta Cryst. (2007). D63, 119-125  [ doi:10.1107/S0907444906042442 ]

An automated image-collection system for crystallization experiments using SBS standard microplates

E. Brostromer, J. Nan and X.-D. Su

Synopsis: An in-house-developed automated imaging system for SBS microplate experiments has been designed and constructed, together with a web-based image-collection and storage database.

Online 16 January 2007

 

Acta Cryst. (2007). D63, 126-134  [ doi:10.1107/S0907444906043654 ]

Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase

Y. Zhang, M. H. el Kouni and S. E. Ealick

Synopsis: T. gondii adenosine kinase substrate analogs with hydrophobic substituents at the 6-position result in a partially closed conformation of the enzyme.

PDB reference: 2a9y

Online 16 January 2007

 

Acta Cryst. (2007). D63, 135-148  [ doi:10.1107/S0907444906043812 ]

The first structure of a cold-active catalase from Vibrio salmonicida at 1.96 Å reveals structural aspects of cold adaptation

E. K. Riise, M. S. Lorentzen, R. Helland, A. O. Smalås, H.-K.S. Leiros and N. P. Willassen

Synopsis: The crystal structure of the cold-adapted catalase from the fish-pathogenic bacterium V. salmonicida (VSC) has been solved to 1.96 Å, and an extensive structural comparison of VSC and the catalase from the mesophilic human pathogen Proteus mirabilis has been performed.

PDB reference: 2isa

Online 16 January 2007

 

Acta Cryst. (2007). D63, 149-159  [ doi:10.1107/S0907444906044271 ]

Structure determination by multiwavelength anomalous diffraction of aclacinomycin oxidoreductase: indications of multidomain pseudomerohedral twinning

A. Sultana, I. Alexeev, I. Kursula, P. Mäntsälä, J. Niemi and G. Schneider

Synopsis: Crystals of aclacinomycin oxidoreductase are pseudomerohedrally twinned and are most likely to contain six twin domains. The structure was determined by multiwavelength anomalous diffraction using data from selenomethionine-substituted crystals.

PDB reference: 2ipi

Online 16 January 2007

 

Acta Cryst. (2007). D63, 160-170  [ doi:10.1107/S0907444906044453 ]

Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures

A. Volkov, M. Messerschmidt and P. Coppens

Synopsis: Application of the University at Buffalo theoretical databank of aspherical pseudoatoms to the refinement of experimental X-ray data from polypeptide structures significantly improves the resulting molecular geometries, residual Fourier difference maps, atomic anisotropic displacement parameters and phases of reflections. Implications for the refinement of protein data are discussed.

Online 16 January 2007

 

Acta Cryst. (2007). D63, 171-178  [ doi:10.1107/S0907444906044465 ]

pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study

A. Ciulli, C. M. C. Lobley, K. L. Tuck, A. G. Smith, T. L. Blundell and C. Abell

Synopsis: A combined crystallographic, calorimetric and mutagenic study has been used to show how changes in pH give rise to two distinct binding modes of 2'-phospho-ADP-ribose to ketopantoate reductase.

PDB reference: 1yon

Online 16 January 2007

 

Acta Cryst. (2007). D63, 179-187  [ doi:10.1107/S0907444906045471 ]

The -propeller domain of the trilobed protease from Pyrococcus furiosus reveals an open Velcro topology

J. Bosch, T. Tamura, N. Tamura, W. Baumeister and L.-O. Essen

Synopsis: A high-molecular-weight protease complex called trilobed protease (TLP) was recently discovered in the archaeon P. furiosus. The crystal structure of the N-terminal -propeller domain of the trilobed protease at 2 Å resolution shows that the trilobed protease utilizes this accessory domain to control substrate access to the active site.

PDB reference: 2gop

Online 16 January 2007

 

Acta Cryst. (2007). D63, 188-196  [ doi:10.1107/S0907444906045793 ]

Ab initio molecular-replacement phasing for symmetric helical membrane proteins

P. Strop, M. R. Brzustowicz and A. T. Brunger

Synopsis: An ab initio molecular-replacement method for phasing X-ray diffraction data for symmetric helical membrane proteins has been developed. The described method is based on generating all possible orientations of idealized transmembrane helices and using each model in a molecular-replacement search.

Online 16 January 2007

 

Acta Cryst. (2007). D63, 197-205  [ doi:10.1107/S090744490604618X ]

Structure of the putative mutarotase YeaD from Salmonella typhimurium: structural comparison with galactose mutarotases

S. Chittori, D. K. Simanshu, H. S. Savithri and M. R. N. Murthy

Synopsis: The crystal structure of the putative mutarotase YeaD from S. typhimurium has been determined in orthorhombic and monoclinic crystal forms at 1.9 and 2.5 Å resolution, respectively. Comparison of the sequence and structure of YeaD with those of galactose mutarotases (GalMs) has allowed the identification of active-site residues and suggests plausible substrate specificity.

PDB references: 2hta and 2htb

Online 16 January 2007

 

Acta Cryst. (2007). D63, 206-220  [ doi:10.1107/S0907444906046488 ]

Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii

P. Gayathri, M. Banerjee, A. Vijayalakshmi, S. Azeez, H. Balaram, P. Balaram and M. R. N. Murthy

Synopsis: The crystal structure of a recombinant triosephosphate isomerase (TIM) from the archaeabacterium M. jannaschii has been determined at a resolution of 2.3 Å using X-ray diffraction data from a tetartohedrally twinned crystal. M. jannaschii TIM (MjTIM) is tetrameric, as is the case for two other structurally characterized archaeal TIMs, and the unliganded structure has a completely disordered active-site loop.

PDB reference: 2h6r

Online 16 January 2007

 

Acta Cryst. (2007). D63, 221-229  [ doi:10.1107/S0907444906048712 ]

Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography

C. Addy, M. Ohara, F. Kawai, A. Kidera, M. Ikeguchi, S. Fuchigami, M. Osawa, I. Shimada, S.-Y. Park, J. R. H. Tame and J. G. Heddle

Synopsis: The crystal structure of a binding-site mutant of NikA shows nickel binding to a second site.

PDB reference: 2noo

Online 16 January 2007

 

Acta Cryst. (2007). D63, 230-239  [ doi:10.1107/S0907444906049262 ]

Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis

N. Kondo, N. Nakagawa, A. Ebihara, L. Chen, Z.-J. Liu, B.-C. Wang, S. Yokoyama, S. Kuramitsu and R. Masui

Synopsis: Here, the crystal structure of Tt-dNTPase has been determined at 2.2 Å resolution, representing the first report of the tertiary structure of a dNTPase homologue belonging to the HD superfamily, a diverse group of metal-dependent phosphohydrolases that includes a variety of uncharacterized proteins.

PDB reference: 2dqb

Online 16 January 2007

 

Acta Cryst. (2007). D63, 240-248  [ doi:10.1107/S090744490604947X ]

Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites

I. Bento, C. Peixoto, V. N. Zaitsev and P. F. Lindley

Synopsis: The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature.

PDB reference: 2j5w

Online 16 January 2007

 

Acta Cryst. (2007). D63, 249-259  [ doi:10.1107/S0907444906050530 ]

Insights into the inter-ring plasticity of caseinolytic proteases from the X-ray structure of Mycobacterium tuberculosis ClpP1

H. Ingvarsson, M. J. Maté, M. Högbom, D. Portnoï, N. Benaroudj, P. M. Alzari, M. Ortiz-Lombardía and T. Unge

Synopsis: The crystal structure of M. tuberculosis caseinolytic protease subunit 1 (ClpP1) is reported. This structure shows novel inter-monomer arrangements that suggest a further source of flexibility for the inter-ring interactions of ClpP proteins.

PDB references: 2c8t, 2ce3 and 2cby

Online 16 January 2007

 

Acta Cryst. (2007). D63, 260-265  [ doi:10.1107/S0907444906042910 ]

High-resolution diffracting crystals of intrinsically active p38 MAP kinase: a case study for low-throughput approaches

R. Diskin, D. Engelberg and O. Livnah

Synopsis: Active p38 MAP kinase mutants caused severe difficulties during crystallization. The main hindrance was found to be protein heterogeneity, which was meticulously resolved by genetically modifying the recombinant protein and optimizing the expression and purification protocols. The success in obtaining crystallizable proteins strongly emphasizes that, in certain cases, high-throughput techniques together with low-throughput approaches, with careful monitoring and analysis of the results, are essential.

Online 16 January 2007

 

Acta Cryst. (2007). D63, 266-269  [ doi:10.1107/S0907444906043435 ]

Structure of the response regulator VicR DNA-binding domain

C.-H. Trinh, Y. Liu, S. E. V. Phillips and M. K. Phillips-Jones

Synopsis: The structure of the DNA-binding domain of the response regulator VicR from E. faecalis has been solved at 1.9 Å resolution. It is very similar to the related domains from PhoB and OmpR, but differs in two loops that may affect transcription activation or DNA-protein interactions.

PDB reference: 2hwv

Online 16 January 2007

 

Acta Cryst. (2007). D63, 270-274  [ doi:10.1107/S0907444906044118 ]

On the precision of calculated solvent-accessible surface areas

M. Novotny, M. Seibert and G. J. Kleywegt

Synopsis: The issue of precision with respect to calculated solvent-accessible surface areas is addressed.

Online 16 January 2007