Biological Crystallography

 

Acta Cryst. (2008). D64, 471-477  [ doi:10.1107/S0907444908003338 ]

Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

C. Tu, Y.-H. Tan, G. Shaw, Z. Zhou, Y. Bai, R. Luo and X. Ji

Synopsis: The impact of hotspot mutation R282Q on the structure of human p53 DNA-binding domain has been characterized by X-ray crystallography and molecular-dynamics simulations.

PDB reference: 2pcx

Online 19 April 2008

 

Acta Cryst. (2008). D64, 478-486  [ doi:10.1107/S0907444908003442 ]

Ultralow-resolution ab initio phasing of filamentous proteins: crystals from a six-Ig fragment of titin as a case study

A. Urzhumtsev, E. von Castelmur and O. Mayans

Synopsis: Low-resolution ab initio phased images of a six-Ig fragment from titin and their a posteriori comparison with the independently elucidated atomic model address the particular challenges that filamentous proteins pose to the low-resolution phasing methodology.

Online 19 April 2008

 

Acta Cryst. (2008). D64, 487-495  [ doi:10.1107/S0907444908004046 ]

Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1

M. A. White, N. Mast, I. Bjorkhem, E. F. Johnson, C. D. Stout and I. A. Pikuleva

Synopsis: Crystallization and analysis of the MIRAS heavy-atom structure solution of human cytochrome P450 46A1 using NaI and CsCl quick soaks.

Online 19 April 2008

 

Acta Cryst. (2008). D64, 496-505  [ doi:10.1107/S0907444908004009 ]

The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD⁺ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family

M. M. Hoque, S. Shimizu, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, M. Tsunoda, H. Amano, T. Sekiguchi and A. Takénaka

Synopsis: The crystal structures of D-3-hydroxybutyrate dehydrogenase from A. faecalis and of its complex with NAD⁺ and acetate suggest the mechanisms of substrate recognition and catalytic reaction. A structural comparison with other enzymes of the short-chain dehydrogenase/reductase family suggests that functional versatility has developed from a common ancestor protein.

PDB references: 2yz7 and 2zea

Online 19 April 2008

 

Acta Cryst. (2008). D64, 506-514  [ doi:10.1107/S0907444908004265 ]

Optimization of buffer solutions for protein crystallization

R. A. Gosavi, T. C. Mueser and C. A. Schall

Synopsis: Increasing the solubility of proteins through buffer optimization and addition of glycerol to values above that found in a standard chromatography buffer led to a statistically significant improvement in crystallization screening results. Estimation of solubility in buffer provides a means for selection of an initial protein concentration for successful screening.

Online 19 April 2008

 

Acta Cryst. (2008). D64, 515-524  [ doi:10.1107/S0907444908004319 ]

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias

T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. Read, P. H. Zwart and L.-W. Hung

Synopsis: An OMIT procedure is presented that has the benefits of iterative model building density modification and refinement yet is essentially unbiased by the atomic model that is built.

Online 19 April 2008

    

Acta Cryst. (2008). D64, 525-531  [ doi:10.1107/S0907444908004277 ]

A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry

K. Kato, H. Tanaka, T. Sumizawa, M. Yoshimura, E. Yamashita, K. Iwasaki and T. Tsukihara

Synopsis: A vault from rat liver was crystallized in space group C2. Rotational symmetry searches indicated that the particle has 39-fold dihedral symmetry.

Online 19 April 2008

 

Acta Cryst. (2008). D64, 532-542  [ doi:10.1107/S0907444908004538 ]

Structure of monkey dimeric dihydrodiol dehydrogenase in complex with isoascorbic acid

V. Carbone, R. Sumii, S. Ishikura, Y. Asada, A. Hara and O. El-Kabbani

Synopsis: The crystal structure of monkey dimeric dihydrodiol dehydrogenase complexed with the inhibitor isoascorbic acid has been determined at 2.59 Å resolution.

PDB reference: 2poq

Online 19 April 2008

 

Acta Cryst. (2008). D64, 543-550  [ doi:10.1107/S0907444908004976 ]

Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant

M. Sherawat, D. R. Tolan and K. N. Allen

Synopsis: The X-ray crystallographic structure of a dimer variant of fructose-1,6-bisphosphate aldolase demonstrates a stable oligomer that mirrors half of the native tetramer. The presence of product demonstrates that this is an active form.

PDB reference: 3bv4

Online 19 April 2008

 

Acta Cryst. (2008). D64, 551-560  [ doi:10.1107/S090744490800512X ]

Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources

P. S. Kaushal, R. K. Talawar, P. D. V. Krishna, U. Varshney and M. Vijayan

Synopsis: Uracil-DNA glycosylase from M. tuberculosis exhibits differences from the enzymes from other sources, particularly in the catalytic loops and the N- and C-terminal regions. The central region of the molecule is relatively invariant in sequence and structure among proteins from different organisms.

PDB reference: 2zhx

Online 19 April 2008

 

Acta Cryst. (2008). D64, 561-566  [ doi:10.1107/S0907444908006021 ]

A new rotation function for molecular replacement by using both the self and cross Patterson vectors

F. Jiang

Synopsis: A new rotation function has been designed for the molecular-replacement method in real space in which both the self and cross Patterson vectors are matched. This rotation function is shown to be sufficiently sensitive to detect a two-helix fragment in a myoglobin crystal structure.

Online 19 April 2008

 

Acta Cryst. (2008). D64, 567-588  [ doi:10.1107/S0907444908006082 ]

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case

B. Guillot, C. Jelsch, A. Podjarny and C. Lecomte

Synopsis: A constrained refinement of the valence electron density against ultrahigh-resolution synchrotron X-ray diffraction data was performed using a multipolar atom model for the protein main-chain and side-chain atoms.

Online 19 April 2008

 

Acta Cryst. (2008). D64, 589-594  [ doi:10.1107/S0907444908003120 ]

Structures of the human ceramide activator protein saposin D

K. Popovic and G. G. Privé

Synopsis: Structures of human saposin D are presented in two crystal forms at 1.3 and 2.0 Å. The protein adopts the compact monomeric saposin fold as seen in saposins A and C.

PDB references: 3bqp and 3bqq

Online 19 April 2008

 

Acta Cryst. (2008). D64, 595-606  [ doi:10.1107/S0907444908007853 ]

MAD phasing using the (Ta₆Br₁₂)²⁺ cluster: a retrospective study

O. Pasternak, A. Bujacz, J. Biesiadka, G. Bujacz, M. Sikorski and M. Jaskolski

Synopsis: The first case of authentic structure determination by MAD phasing using high-resolution data from a (Ta₆Br₁₂)²⁺ derivative is analyzed to provide practical hints for the application of this useful phasing agent.

PDB reference: 3c0v

Online 19 April 2008

 

Acta Cryst. (2008). D64, 607-610  [ doi:10.1107/S0907444908005477 ]

Structure of isochorismate synthase in complex with magnesium

J. F. Parsons, K. M. Shi and J. E. Ladner

Synopsis: The structure of the menaquinone-specific isochorismate synthase (MenF) from Escherichia coli has been refined at a resolution of 2.0 Å in complex with magnesium. The magnesium-bound structure has a well defined and organized active site which better represents the active conformation of the enzyme than the currently available structure.

PDB references: 3bzm and 3bzn

Online 19 April 2008