Acta Crystallographica Section D

Biological Crystallography

Volume 64, Part 4 (April 2008)


	Cover illustration: The tertiary structure of hepatitis C virus IRES subdomain IIa showing an L-shaped helical conformation (p. 436). Two uridine bases are rotated out into the solvent altering the conformation of the RNA backbone. This unique RNA structure is stabilized by bound divalent metal ions. The RNA backbone is shown as blue; Sr²⁺ atoms are colored orange.

editorial
research papers
short communications

editorial

Acta Cryst. (2008). D64, 337-338 [ doi:10.1107/S0907444908004915 ]

Deposition of diffraction images to be discussed at the Open Meeting of the Commission on Biological Macromolecules of the IUCr in Osaka

E. N. Baker, Z. Dauter, M. Guss and H. Einspahr

Online 19 March 2008

research papers

Acta Cryst. (2008). D64, 339-353 [ doi:10.1107/S0907444907068217 ]

Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin

T. M. Bandeiras, R. C. Hillig, P. M. Matias, U. Eberspaecher, J. Fanghänel, M. Thomaz, S. Miranda, K. Crusius, V. Pütter, P. Amstutz, M. Gulotti-Georgieva, H. K. Binz, C. Holz, A. A. P. Schmitz, C. Lang, P. Donner, U. Egner, M. A. Carrondo and B. Müller-Tiemann

Synopsis: The crystal structure of the kinase domain of wild-type polo-like kinase 1 (Plk-1) has been determined after identifying suitable domain borders via a parallel cloning and expression approach and upon generation of a selective designed ankyrin-repeat protein (DARPin) which served as a crystallization tool.

PDB reference: 2v5q

Online 19 March 2008

Acta Cryst. (2008). D64, 354-367 [ doi:10.1107/S0907444907068849 ]

Towards a rational approach for heavy-atom derivative screening in protein crystallography

J. Agniswamy, M. G. Joyce, C. H. Hammer and P. D. Sun

Synopsis: Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue.

Online 19 March 2008

Acta Cryst. (2008). D64, 368-376 [ doi:10.1107/S0907444908000097 ]

Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida

B. Altermark, R. Helland, E. Moe, N. P. Willassen and A. O. Smalås

Synopsis: The adaptation of enzymes to low temperatures and seawater salinity has been investigated on a structural level. The crystal structure of V. salmonicida endonuclease I is presented and compared with the corresponding enzyme structures from V. cholerae and V. vulnificus.

PDB reference: 2pu3

Online 19 March 2008

Acta Cryst. (2008). D64, 377-382 [ doi:10.1107/S0907444908000474 ]

Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii

E. V. Soriano, D. E. McCloskey, C. Kinsland, A. E. Pegg and S. E. Ealick

Synopsis: The crystal structures of two arginine decarboxylase mutant proteins provide insights into the mechanisms of pyruvoyl-group formation and the decarboxylation reaction.

PDB references: 2qqc and 2qqd

Online 19 March 2008

Acta Cryst. (2008). D64, 383-396 [ doi:10.1107/S090744490800070X ]

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

J. L. Knight, Z. Zhou, E. Gallicchio, D. M. Himmel, R. A. Friesner, E. Arnold and R. M. Levy

Synopsis: Torsion-angle sampling, as implemented in the Protein Local Optimization Program (PLOP), is used to generate multiple structurally variable single-conformer models which are in good agreement with X-ray data. An ensemble-refinement approach to differentiate between positional uncertainty and conformational heterogeneity is proposed.

Online 19 March 2008

Acta Cryst. (2008). D64, 397-406 [ doi:10.1107/S0907444908000723 ]

Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2

S. Kishishita, K. Shimizu, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama and N. Kunishima

Synopsis: The crystal structures of the homodimeric diphthine synthases from A. pernix K1 and P. horikoshii OT3 were determined by X-ray diffraction. The present study suggests the biological importance of the asymmetry in the dimeric structure of this enzyme for the effective recognition of a large substrate, EF-2.

PDB references: 1wde and 1wng

Online 19 March 2008

Acta Cryst. (2008). D64, 407-415 [ doi:10.1107/S0907444908001091 ]

A mixture of fortunes: the curious determination of the structure of Escherichia coli BL21 Gab protein

B. Lohkamp and D. Dobritzsch

Synopsis: A protein from E. coli was crystallized from an inhomogeneous protein sample and identified as Gab protein by structure determination. The obtained structure is compared with a previously deposited structure of the same protein and potential ligand binding is discussed.

PDB reference: 2r6s

Online 19 March 2008

Acta Cryst. (2008). D64, 416-424 [ doi:10.1107/S0907444908001558 ]

A knowledge-driven approach for crystallographic protein model completion

K. Joosten, S. X. Cohen, P. Emsley, W. Mooij, V. S. Lamzin and A. Perrakis

Synopsis: A novel method that uses the conformational distribution of C atoms in known structures is used to build short missing regions (`loops') in protein models. An initial tree of possible loop paths is pruned according to structural and electron-density criteria and the most likely loop conformation(s) are selected and built.

Online 19 March 2008

Acta Cryst. (2008). D64, 425-435 [ doi:10.1107/S0907444908001741 ]

A 7 µm mini-beam improves diffraction data from small or imperfect crystals of macromolecules

R. Sanishvili, V. Nagarajan, D. Yoder, M. Becker, S. Xu, S. Corcoran, D. L. Akey, J. L. Smith and R. F. Fischetti

Synopsis: An X-ray mini-beam of 8 × 6 µm cross-section was used to collect diffraction data from protein microcrystals with volumes as small as 150-300 µm³. The benefits of the mini-beam for experiments with small crystals and with large inhomogeneous crystals are investigated.

Online 19 March 2008

Acta Cryst. (2008). D64, 436-443 [ doi:10.1107/S0907444908002011 ]

Structure of hepatitis C virus IRES subdomain IIa

Q. Zhao, Q. Han, C. R. Kissinger, T. Hermann and P. A. Thompson

Synopsis: The structure of the HCV IRES subdomain IIa has been solved at 2.3 Å resolution in the presence of Mg²⁺ and Sr²⁺. The results provide additional insight into the specific interactions that stabilize the unique conformation.

PDB references: 2pn3 and 2pn4

Online 19 March 2008

Acta Cryst. (2008). D64, 444-453 [ doi:10.1107/S0907444908002850 ]

Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state

K. Shimizu, C. Kuroishi, M. Sugahara and N. Kunishima

Synopsis: The crystal structure of peptidyl-tRNA hydrolase 2 from P. horikoshii OT3 has been determined in two different crystal forms. The present study suggests the practical importance of the dimeric structure for tRNA binding.

PDB references: 1wn2 and 2d3k

Online 19 March 2008

Acta Cryst. (2008). D64, 454-465 [ doi:10.1107/S0907444908003351 ]

Multiple crystal structures of actin dimers and their implications for interactions in the actin filament

M. R. Sawaya, D. S. Kudryashov, I. Pashkov, H. Adisetiyo, E. Reisler and T. O. Yeates

Synopsis: Multiple crystal structures are reported of cross-linked actin dimers. Interactions that are conserved across crystal structures suggest detailed interactions that are likely to be present in F-actin filaments.

PDB references: 2q1n, 2q31 and 2q36

Online 19 March 2008