Acta Cryst. (2012). D68, 497-504
[ doi:10.1107/S0907444912002740 ]

Beyond the detergent effect: a binding site for sodium dodecyl sulfate (SDS) in mammalian apoferritin

R. Liu, W. Bu, J. Xi, S. R. Mortazavi, J. C. Cheung-Lau, I. J. Dmochowski and P. J. Loll

Synopsis: Using X-ray crystallography and isothermal titration calorimetry, we show that sodium dodecyl sulfate (SDS) binds specifically to a pre-formed internal cavity in horse-spleen apoferritin.

PDB reference: 3u90

Online 17 April 2012

 

Acta Cryst. (2012). D68, 505-510
[ doi:10.1107/S0907444912002946 ]

X-ray-excited optical luminescence of protein crystals: a new tool for studying radiation damage during diffraction data collection

R. L. Owen, B. A. Yorke and A. R. Pearson

Synopsis: Macromolecular crystals luminesce during X-ray irradiation. This luminescence, and how it changes as a function of absorbed dose, has been characterized for several different proteins.

Online 17 April 2012

 

Acta Cryst. (2012). D68, 511-520
[ doi:10.1107/S0907444912003551 ]

Peptide inhibitors of botulinum neurotoxin serotype A: design, inhibition, cocrystal structures, structure-activity relationship and pharmacophore modeling

G. Kumar, D. Kumaran, S. A. Ahmed and S. Swaminathan

Synopsis: Botulinum neurotoxins have been declared as a Category A agent by the Centers of Disease Control and Prevention owing to their extremely poisonous nature and are potential bioweapon and bioterrorism agents. Towards the discovery of antidotes, structures of inhibitory peptide-enzyme complexes were determined, the structure-activity relationship was determined and a pharmacophore was developed.

PDB references: 3qw5, 3qw6, 3qw7 and 3qw8

Online 17 April 2012

 

Acta Cryst. (2012). D68, 521-530
[ doi:10.1107/S0907444912004490 ]

S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS

H. Ru, L. Zhao, W. Ding, L. Jiao, N. Shaw, W. Liang, L. Zhang, L.-W. Hung, N. Matsugaki, S. Wakatsuki and Z.-J. Liu

Synopsis: A comparative analysis of sulfur phasing of death receptor 6 (DR6) using data collected at wavelengths of 2.0 and 2.7 Å is presented. SAXS analysis of unliganded DR6 defines a dimer as the minimum physical unit in solution.

PDB references: 3u3p, 3u3q, 3u3s, 3u3v and 3u3t

Online 17 April 2012

 

Acta Cryst. (2012). D68, 531-540
[ doi:10.1107/S090744491200491X ]

Novel -structure of YLR301w from Saccharomyces cerevisiae

K.-H. Kim, H. J. Ahn, W.-K. Lee, C. Lee, M.-H. Yu and E. E. Kim

Synopsis: The structure of the uncharacterized protein YLR301w is reported.

PDB reference: 3rby

Online 17 April 2012

 

Acta Cryst. (2012). D68, 541-552
[ doi:10.1107/S0907444912004817 ]

An analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases

D. Bailey, E. P. Carpenter, A. Coker, S. Coker, J. Read, A. T. Jones, P. Erskine, C. F. Aguilar, M. Badasso, L. Toldo, F. Rippmann, J. Sanz-Aparicio, A. Albert, T. L. Blundell, N. B. Roberts, S. P. Wood and J. B. Cooper

Synopsis: A number of native and inhibitor-complexed aspartic proteinase crystal structures are reported. Analysis of the structure of native endothiapepsin in the same crystal form as that adopted by the majority of inhibitor complexes of this enzyme reveals that the rigid-body movement previously attributed to inhibitor binding may instead be at least partly a consequence of crystal packing involving sulfate anions.

PDB references: 3uri, 3urj, 3url and 3utl

Online 17 April 2012

 

Acta Cryst. (2012). D68, 553-563
[ doi:10.1107/S0907444912004829 ]

Structure of phosphoserine aminotransferase from Mycobacterium tuberculosis

F. Coulibaly, E. Lassalle, H. M. Baker and E. N. Baker

Synopsis: The crystal structure of phosphoserine aminotransferase, an essential enzyme for serine biosynthesis in M. tuberculosis, has been solved at 1.5 Å resolution. The structure reveals differences in the substrate-binding region when compared with the equivalent human enzyme, suggesting opportunities for structure-based drug design.

PDB references: 2fyf and 3vom

Online 17 April 2012

 

Acta Cryst. (2012). D68, 564-577
[ doi:10.1107/S0907444912005343 ]

Structural changes caused by radiation-induced reduction and radiolysis: the effect of X-ray absorbed dose in a fungal multicopper oxidase

E. De la Mora, J. E. Lovett, C. F. Blanford, E. F. Garman, B. Valderrama and E. Rudino-Pinera

Synopsis: Radiation-induced reduction, radiolysis of copper sites and the effect of pH value together with the concomitant geometrical distortions of the active centres were analysed in several fungal (C. gallica) laccase structures collected at cryotemperature. This study emphasizes the importance of careful interpretation when the crystallographic structure of a metalloprotein is described.

PDB references: 4a2d, 4a2e, 4a2f, 4a2g and 4a2h

Online 17 April 2012

 

Acta Cryst. (2012). D68, 578-583
[ doi:10.1107/S0907444912006348 ]

Ribosome engineering to promote new crystal forms

M. Selmer, Y.-G. Gao, A. Weixlbaumer and V. Ramakrishnan

Synopsis: Truncation of ribosomal protein L9 in T. thermophilus allows the generation of new crystal forms and the crystallization of ribosome-GTPase complexes.

Online 17 April 2012

 

Acta Cryst. (2012). D68, 584-591
[ doi:10.1107/S0907444912006427 ]

Sensitivity of lysozyme crystallization to minute variations in concentration

R.-Q. Chen, D.-C. Yin, Q.-Q. Lu, J.-Y. Shi and X.-L. Ma

Synopsis: The effect of minute variations in the concentration of the protein solution on the crystallization success rate of lysozyme was investigated and it was found that a very small variation in protein concentration of as low as 0.13% (0.026 mg ml^-1 in the current study) could exert a significant effect on the crystallization of lysozyme.

Online 17 April 2012

 

Acta Cryst. (2012). D68, 592-600
[ doi:10.1107/S0907444912006749 ]

In situ macromolecular crystallography using microbeams

D. Axford, R. L. Owen, J. Aishima, J. Foadi, A. W. Morgan, J. I. Robinson, J. E. Nettleship, R. J. Owens, I. Moraes, E. E. Fry, J. M. Grimes, K. Harlos, A. Kotecha, J. Ren, G. Sutton, T. S. Walter, D. I. Stuart and G. Evans

Synopsis: A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described.

Online 17 April 2012

 

Acta Cryst. (2012). D68, 601-612
[ doi:10.1107/S0907444912006907 ]

Structural studies of the effect that dimethyl sulfoxide (DMSO) has on cisplatin and carboplatin binding to histidine in a protein

S. W. M. Tanley, A. M. M. Schreurs, L. M. J. Kroon-Batenburg, J. Meredith, R. Prendergast, D. Walsh, P. Bryant, C. Levy and J. R. Helliwell

Synopsis: The anticancer complexes cisplatin and carboplatin target the DNA major groove, but have toxic side effects. It is shown that in the presence of DMSO two molecules of either cisplatin or carboplatin bind to its His15 residue. The observation of this effect with DMSO, a widely used super-solvent for drug delivery, should be considered in toxicity assessments of these drugs.

PDB references: 4dd0, 4dd1, 4dd2, 4dd3, 4dd4, 4dd6, 4dd7, 4dd9, 4dda, 4ddb and 4ddc

Online 17 April 2012

 

Acta Cryst. (2012). D68, 613-617
[ doi:10.1107/S0907444912004799 ]

Notes of a protein crystallographer: on the high-resolution structure of the PDB growth rate

C. Abad-Zapatero

Synopsis: A detailed analysis of the growth rate of the PDB is presented that suggests appreciable changes in the deposition rates for certain periods, possibly related to technical innovations or to sociological events in the development of the field of macromolecular crystallography.

Online 17 April 2012