Biological Crystallography

 

Acta Cryst. (2009). D65, 1013-1020  [ doi:10.1107/S0907444909023762 ]

Overproduction, purification and structure determination of human dual-specificity phosphatase 14

G. T. Lountos, J. E. Tropea, S. Cherry and D. S. Waugh

Synopsis: The crystal structure of human dual-specificity phosphatase 14, DUSP14 (MKP6), in complex with a phosphate ion has been determined and refined to 1.88 Å resolution.

PDB reference: 2wgp

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1021-1031  [ doi:10.1107/S0907444909026547 ]

Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity

S. C. Gay, I. H. Segel and A. J. Fisher

Synopsis: APS kinase from Thiobacillus denitrificans contains an inactive N-terminal ATP sulfurylase domain. The structure presented unveils the first hexameric assembly for an APS kinase, and reveals that structural changes in the N-terminal domain disrupt the ATP sulfurylase active site thus prohibiting activity.

PDB reference: 3cr8

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1032-1041  [ doi:10.1107/S0907444909027012 ]

End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures

T. S. Ghosh, S. K. Chaitanya and R. Sankararamakrishnan

Synopsis: New classes of helix-helix interactions in protein structures are reported in which interactions only occur at the terminal regions or between the terminal region of one helix and the middle region of another helix.

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1042-1050  [ doi:10.1107/S090744490902770X ]

A neutron crystallographic analysis of T₆ porcine insulin at 2.1 Å resolution

W. Iwai, T. Yamada, K. Kurihara, Y. Ohnishi, Y. Kobayashi, I. Tanaka, H. Takahashi, R. Kuroki, T. Tamada and N. Niimura

Synopsis: The charge balance and hydrogen-bonding network at the core of the insulin T₆ hexamer have been investigated by neutron diffraction analysis at 2.1 Å resolution.

PDB reference: 3fhp

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1051-1061  [ doi:10.1107/S0907444909028078 ]

A multivariate likelihood SIRAS function for phasing and model refinement

P. Skubák, G. Murshudov and N. S. Pannu

Synopsis: The application of a multivariate likelihood function to a single isomorphous replacement with anomalous scattering experiment improves phasing and automated model building with iterative refinement in the test cases shown.

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1062-1073  [ doi:10.1107/S0907444909029163 ]

Effects of impurities on membrane-protein crystallization in different systems

C. A. Kors, E. Wallace, D. R. Davies, L. Li, P. D. Laible and P. Nollert

Synopsis: The effects of commonly encountered impurities on various membrane-protein crystallization regimes are investigated and it is found that the lipidic cubic phase crystallization methodology is the most robust, tolerating protein contamination levels of up to 50%, with little effect on crystal quality. If generally applicable, this tolerance may be exploited (i) in initial crystallization trials to determine the `crystallizability' of a given membrane-protein and (ii) to subject partially pure membrane-protein samples to crystallization trials.

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1074-1080  [ doi:10.1107/S0907444909029436 ]

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation

N. W. Moriarty, R. W. Grosse-Kunstleve and P. D. Adams

Synopsis: A new software system for automated ligand coordinate and restraint generation is presented.

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1081-1088  [ doi:10.1107/S0907444909029321 ]

Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment

E. Morgunova, F. C. Gray, S. A. MacNeill and R. Ladenstein

Synopsis: The crystal structure of PCNA from the halophilic archaeon H. volcanii reveals specific features of the charge distribution on the protein surface that reflect adaptation to a high-salt environment and suggests a different type of interaction with DNA in halophilic PCNAs.

PDB reference: 3hi8

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1089-1097  [ doi:10.1107/S0907444909029643 ]

On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination

S. Panjikar, V. Parthasarathy, V. S. Lamzin, M. S. Weiss and P. A. Tucker

Synopsis: The combination of molecular replacement and single-wavelength anomalous diffraction improves the performance of automated structure determination with Auto-Rickshaw.

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1098-1106  [ doi:10.1107/S0907444909029710 ]

Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions

Y. Kitamura, A. Ebihara, Y. Agari, A. Shinkai, K. Hirotsu and S. Kuramitsu

Synopsis: The structures of five forms of D-alanine-D-alanine ligase from T. thermophilus HB8 showed a cumulative conformational change of the molecular structure through the induced rotation of the central domain in concert with a local conformational change of three loops. The active-site structures shed light on the catalytic mechanism and the roles of the conformational change.

PDB references: 2yzg, 2yzn, 2zdg, 2zdh and 2zdq

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1107-1117  [ doi:10.1107/S0907444909030613 ]

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

H. van den Bedem, A. Dhanik, J.-C. Latombe and A. M. Deacon

Synopsis: A new algorithm that automatically models discrete heterogeneity in X-ray data demonstrates that the variability observed at high resolution can be adequately represented by including correlated structural features in protein models. The algorithm is based on simultaneous exploration of a very large number of alternative interpretations of electron-density maps.

Online 16 September 2009

 

Acta Cryst. (2009). D65, 1118-1125  [ doi:10.1107/S0907444909031011 ]

A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

D. A. Breustedt, L. Chatwell and A. Skerra

Synopsis: The crystal structure of tear lipocalin determined in space group P2₁ revealed large structural deviations from the previously solved X-ray structure in space group C2, especially in the loop region and adjoining parts of the -barrel which give rise to the ligand-binding site. These findings illustrate a novel mechanism for promiscuity in ligand recognition by the lipocalin protein family.

PDB reference: 3eyc

Online 16 September 2009