Biological Crystallography

 

Acta Cryst. (2012). D68, 875-882  [ doi:10.1107/S0907444912016496 ]

Structure of the catalytic core module of the Chaetomium thermophilum family GH6 cellobiohydrolase Cel6A

A. J. Thompson, T. Heu, T. Shaghasi, R. Benyamino, A. Jones, E. P. Friis, K. S. Wilson and G. J. Davies

Synopsis: The three-dimensional structure of an industrially relevant cellulase in complex with ligands has been determined at a resolution of 1.9 Å.

PDB reference: 4a05

Online 7 July 2012

 

Acta Cryst. (2012). D68, 883-892  [ doi:10.1107/S0907444912016587 ]

Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias

K. Klopffleisch, O.-G. Issinger and K. Niefind

Synopsis: A low-resolution structure of the catalytic subunit CK2 of human protein kinase CK2 (formerly known as casein kinase 2) in complex with the ATP-competitive inhibitor resorufin is presented. An overview of all published human CK2 crystal packings serves as the basis for a discussion of the factors that determine whether the open or the closed hinge/helix D conformation is adopted.

PDB references: 3u9c and 3u87

Online 7 July 2012

 

Acta Cryst. (2012). D68, 893-900  [ doi:10.1107/S0907444912016617 ]

Nanolitre-scale crystallization using acoustic liquid-transfer technology

A. G. Villaseñor, A. Wong, A. Shao, A. Garg, T. J. Donohue, A. Kuglstatter and S. F. Harris

Synopsis: Acoustic droplet ejection achieves precise, tipless, non-invasive transfer of diverse aqueous solutions, enabling nanolitre-scale crystallization trials. The rapid and scalable technique demonstrated successful crystal growth with diverse targets in drop volumes as small as 20 nl.

Online 17 July 2012

 

Acta Cryst. (2012). D68, 901-908  [ doi:10.1107/S0907444912016447 ]

An engineered PII protein variant that senses a novel ligand: atomic resolution structure of the complex with citrate

K. Zeth, O. Fokina and K. Forchhammer

Synopsis: A mutant variant of the Synechococcus elongatus PII protein (PII-I86N) has been identified to have impaired 2-oxoglutarate binding. Here, the PII-I86N variant was cocrystallized in the presence of ATP, magnesium and citrate and its structure was solved at a resolution of 1.05 Å.

PDB reference: 4aff

Online 17 July 2012

 

Acta Cryst. (2012). D68, 909-919  [ doi:10.1107/S0907444912016459 ]

The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases with a range of C-terminal sequences

I. Raj, S. Kumar and S. Gourinath

Synopsis: O-Acetylserine sulfhydrylase (OASS) from L. donovani can bind to serine acetyltransferase (SAT) C-terminus mimicking peptides with a range of bulkiness; the strength of these interactions correlates with the size of the peptide side chains and the size of the active-site cleft. Differences in the interactions of OASS and SAT from various species may be explained by the size of the active-site cleft.

PDB references: 3spx, 3t4p and 3tbh

Online 7 July 2012

 

Acta Cryst. (2012). D68, 920-926  [ doi:10.1107/S0907444912017210 ]

Structures of the -class carbonic anhydrase homologue YrdA suggest a possible allosteric switch

H.-M. Park, J.-H. Park, J.-W. Choi, J. Lee, B. Y. Kim, C.-H. Jung and J.-S. Kim

Synopsis: Crystal structures of YrdA from E. coli show conformations that have not been reported for -class carbonic anhydrase family proteins.

PDB references: 3tio and 3tis

Online 7 July 2012

 

Acta Cryst. (2012). D68, 927-934  [ doi:10.1107/S0907444912017143 ]

Structural plasticity of tubulin assembly probed by vinca-domain ligands

F. M. Ranaivoson, B. Gigant, S. Berritt, M. Joullié and M. Knossow

Synopsis: The structure of ustiloxin D bound to tubulin was determined at a resolution which allows interatomic interactions to be defined and provides a basis for the structure-based design of ligands with improved activity. It is also shown how local interactions of vinca-domain ligands with tubulin influence the relative positioning of the latter and lead to the large-scale polymorphism of ligand-mediated tubulin assemblies.

PDB references: 3ut5 and 4eb6

Online 7 July 2012

 

Acta Cryst. (2012). D68, 935-952  [ doi:10.1107/S0907444912017453 ]

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

J. A. Bell, K. L. Ho and R. Farid

Synopsis: All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications.

Online 17 July 2012

 

Acta Cryst. (2012). D68, 953-959  [ doi:10.1107/S0907444912017325 ]

Crystallographic analysis of the conserved C-terminal domain of transcription factor Cdc73 from Saccharomyces cerevisiae reveals a GTPase-like fold

H. Chen, N. Shi, Y. Gao, X. Li, M. Teng and L. Niu

Synopsis: The structure of the C-terminal domain of yCdc73 revealed a GTPase-like fold.

PDB reference: 4dm4

Online 7 July 2012

 

Acta Cryst. (2012). D68, 960-967  [ doi:10.1107/S0907444912017623 ]

The PAD region in the mycobacterial DinB homologue MsPolIV exhibits positional heterogeneity

A. Sharma, V. Subramanian and D. T. Nair

Synopsis: The structure of a Y-family DNA polymerase from Mycobacteria named MsDpo4 along with solution studies suggest that the PAD region is endowed with the ability to adopt multiple orientations. This attribute would allow the enzyme to accommodate alterations in the width of the DNA double helix to facilitate its twin functions of trans-lesion bypass and adaptive mutagenesis.

PDB reference: 4dez

Online 17 July 2012

 

Acta Cryst. (2012). D68, 968-974  [ doi:10.1107/S090744491201815X ]

X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae

A. A. Lashkov, S. E. Sotnichenko, I. I. Prokofiev, A. G. Gabdulkhakov, I. I. Agapov, A. A. Shtil, C. Betzel, A. S. Mironov and A. M. Mikhailov

Synopsis: X-ray structures and in silico models are reported for complexes of the drug 5-fluorouracil with uridine phosphorylases from S. typhimurium and V. cholerae.

PDB reference: 3nsr

Online 17 July 2012

 

Acta Cryst. (2012). D68, 975-984  [ doi:10.1107/S090744491201863X ]

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

S. Brockhauser, O. Svensson, M. W. Bowler, M. Nanao, E. Gordon, R. M. F. Leal, A. Popov, M. Gerring, A. A. McCarthy and A. Gotz

Synopsis: A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services.

Online 17 July 2012

 

Acta Cryst. (2012). D68, 985-995  [ doi:10.1107/S0907444912018549 ]

RCrane: semi-automated RNA model building

K. S. Keating and A. M. Pyle

Synopsis: RCrane is a new tool for the partially automated building of RNA crystallographic models into electron-density maps of low or intermediate resolution. This tool helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides.

Online 17 July 2012

 

Acta Cryst. (2012). D68, 996-1002  [ doi:10.1107/S0907444912018446 ]

Structure of the branched-chain aminotransferase from Streptococcus mutans

J. Ruan, J. Hu, A. Yin, W. Wu, X. Cong, X. Feng and S. Li

Synopsis: The crystal structure of the branched-chain aminotransferase from S. mutans is reported at 1.9 Å resolution.

PDB reference: 4dqn

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1003-1009  [ doi:10.1107/S0907444912018768 ]

A universal indicator dye pH assay for crystallization solutions and other high-throughput applications

J. Newman, R. A. Sayle and V. J. Fazio

Synopsis: A rapid plate-based pH assay has been developed that takes advantage of the automation available in a protein-crystallization laboratory.

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1010-1018  [ doi:10.1107/S0907444912019580 ]

Proline: Mother Nature's cryoprotectant applied to protein crystallography

T. A. Pemberton, B. R. Still, E. M. Christensen, H. Singh, D. Srivastava and J. J. Tanner

Synopsis: The amino acid L-proline is shown to be a good cryoprotectant for protein crystals. Four examples are provided; the range of proline used for cryoprotection is 2.0-3.0 M.

PDB references: 4e3u, 4e3v, 4e3w and 4e3x

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1019-1029  [ doi:10.1107/S0907444912019592 ]

Structural and biochemical characterization of a trapped coenzyme A adduct of Caenorhabditis elegans glucosamine-6-phosphate N-acetyltransferase 1

H. C. Dorfmueller, W. Fang, F. V. Rao, D. E. Blair, H. Attrill and D. M. F. van Aalten

Synopsis: Glucosamine-6-phosphate N-acetyltransferase is an essential enzyme of the eukaryotic UDP-GlcNAc biosynthetic pathway. A crystal structure at 1.55 Å resolution revealed a highly unusual covalent product complex and biochemical studies investigated the function of a fully conserved active-site cysteine.

PDB references: 4ag7 and 4ag9

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1030-1040  [ doi:10.1107/S0907444912019798 ]

The promiscuous binding of the Fyn SH3 domain to a peptide from the NS5A protein

J. M. Martin-Garcia, I. Luque, J. Ruiz-Sanz and A. Camara-Artigas

Synopsis: The promiscuous binding of an NS5A peptide to the Fyn SH3 domain is described.

PDB references: 3ua6 and 3ua7

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1041-1050  [ doi:10.1107/S090744491201997X ]

X-ray structure of p38 bound to TAK-715: comparison with three classic inhibitors

R. Azevedo, M. van Zeeland, H. Raaijmakers, B. Kazemier, J. de Vlieg and A. Oubrie

Synopsis: The first X-ray structure of p38 cocrystallized with TAK-715 is presented, as well as new high-resolution structures of p38 bound to SB-203580, SCIO-469 and VX-745. The impact of crystallization conditions and selectivity profiles on protein conformation is discussed.

PDB references: 3zs5, 3zsg, 3zsh and 3zsi

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1051-1057  [ doi:10.1107/S0907444912020136 ]

High-resolution crystal structure of the isolated ribosomal L1 stalk

S. Tishchenko, A. Gabdulkhakov, N. Nevskaya, A. Sarskikh, O. Kostareva, E. Nikonova, A. Sycheva, S. Moshkovskii, M. Garber and S. Nikonov

Synopsis: The crystal structure of the isolated full-length ribosomal L1 stalk has been solved at high resolution, detailed analysis of L1-rRNA interactions and crystal packing has been carried out.

PDB reference: 3u4m

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1058-1066  [ doi:10.1107/S0907444912020537 ]

Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis

D. Bellini and M. Z. Papiz

Synopsis: Crystallization of RpBphP2-CBD was achieved by homologue-directed mutagenesis via dimer formation in solution by the mutation N136R. Naturally occurring mutations in BphPs correlate well with their observed dimerization properties and suggests a structural diversity within this family.

PDB reference: 4e04

Online 17 July 2012

 

Acta Cryst. (2012). D68, 1067-1070  [ doi:10.1107/S090744491202118X ]

Continuous -turn fold of an alternating alanyl/homoalanyl peptide nucleic acid

J. A. Cuesta-Seijo, J. Zhang, U. Diederichsen and G. M. Sheldrick

Synopsis: The 1.0 Å crystal structure of an alternating L-homoalanyl, D-alanyl peptide nucleic acid reveals a novel tetrameric cage with Watson-Crick pairing of the stacked nucleobases.

PDB reference: 3c1p

Online 17 July 2012