Biological Crystallography

 

Acta Cryst. (2007). D63, 939-940  [ doi:10.1107/S0907444907033458 ]

Separating model optimization and model validation in statistical cross-validation as applied to crystallography

G. J. Kleywegt

Synopsis: A small modification of the standard crystallographic cross-validation protocol (namely, the use of a dormant hold-out set of reflections) is described that makes it possible to separate optimization of the model parameterization and validation of the final model.

Online 17 August 2007

 

Acta Cryst. (2007). D63, 941-950  [ doi:10.1107/S0907444907033847 ]

Quality of protein crystal structures

E. N. Brown and S. Ramaswamy

Synopsis: Structures deposited in the Protein Data Bank were analyzed for their quality using a combination of criteria. These analyses suggest that (i) the quality of protein crystal structures has remained the same over time, (ii) structural genomics generated structures are on average better and (iii) structures published in general science journals are on average significantly poorer in quality compared with the overall database.

Online 17 August 2007

 

Acta Cryst. (2007). D63, 951-960  [ doi:10.1107/S0907444907035160 ]

Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation

M. C. Corbett, M. J. Latimer, T. L. Poulos, I. F. Sevrioukova, K. O. Hodgson and B. Hedman

Synopsis: Single-crystal X-ray absorption spectroscopy (XAS) is used to show the temperature-dependence of X-ray photoreduction of the active site of putidaredoxin, an iron-containing metalloprotein, in a study that highlights the importance of using liquid-helium-based cooling during metalloprotein crystallography experiments and the utility of simultaneous XAS measurements.

Online 17 August 2007

 

Acta Cryst. (2007). D63, 961-968  [ doi:10.1107/S0907444907035470 ]

Production of Slit2 LRR domains in mammalian cells for structural studies and the structure of human Slit2 domain 3

C. Morlot, W. Hemrika, R. A. Romijn, P. Gros, S. Cusack and A. A. McCarthy

Synopsis: Slit2 is a large multidomain protein containing an unusual domain organization of four tandem leucine-rich repeat (LRR) domains at its N-terminus. Here, the crystallization of the second and third LRR domains from human Slit2 and the structure of the third LRR domain are presented.

PDB reference: 2v70

Online 17 August 2007

 

Acta Cryst. (2007). D63, 969-974  [ doi:10.1107/S0907444907036396 ]

The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation

N. Tsesin, A. Kogan, G. Y. Gdalevsky, J.-P. Himanen, R. Cohen-Luria, A. H. Parola, Y. Goldgur and O. Almog

Synopsis: The crystal structure of apo tryptophanase from E. coli (space group F222, unit-cell parameters a = 118.4, b = 120.1, c = 171.2 Å) was determined at 1.9 Å resolution using the molecular-replacement method and was refined to an R factor of 20.3% (R_free = 23.2%).

PDB reference: 2oqx

Online 17 August 2007

 

Acta Cryst. (2007). D63, 975-981  [ doi:10.1107/S0907444907036281 ]

Structural studies of a bifunctional inhibitor of neprilysin and DPP-IV

C. Oefner, S. Pierau, H. Schulz and G. E. Dale

Synopsis: Here, the synthesis and crystal structures of the soluble extracellular domain of human neutral endopeptidase (NEP, residues 52-749) complexed with the NEP, competitive and potent dual NEP/DPP-IV inhibitor MCB3937 are described.

PDB reference: 2qpj

Online 17 August 2007

 

Acta Cryst. (2007). D63, 982-992  [ doi:10.1107/S0907444907036955 ]

Structure of GES-1 at atomic resolution: insights into the evolution of carbapenamase activity in the class A extended-spectrum -lactamases

C. A. Smith, M. Caccamo, K. A. Kantardjieff and S. Vakulenko

Synopsis: The crystal structure of the extended-spectrum -lactamase GES-1 has been solved to 1.1 Å resolution. Imipenem binding is analyzed by flexible-docking simulations into GES-1 and some point-mutant variants producing resistance to carbapenems.

PDB reference: 2qpn

Online 17 August 2007

 

Acta Cryst. (2007). D63, 993-999  [ doi:10.1107/S0907444907036128 ]

An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer

I. J. MacRae and J. A. Doudna

Synopsis: An unusual case of perfect pseudo-merohedral twinning in orthorhombic crystals of the enzyme Dicer is discussed.

PDB reference: 2qvw

Online 17 August 2007

 

Acta Cryst. (2007). D63, 1000-1008  [ doi:10.1107/S0907444907037705 ]

The effect of deuteration on protein structure: a high-resolution comparison of hydrogenous and perdeuterated haloalkane dehalogenase

X. Liu, B. L. Hanson, P. Langan and R. E. Viola

Synopsis: A comparison of hydrogenous and perdeuterated haloalkane dehalogenase shows similar overall structures with only slight alterations in surface regions. However, perdeuteration causes exclusion of a critical water nucleophile from the active site leading to a structure of an inactive, low pH enzyme form.

Online 17 August 2007

 

Acta Cryst. (2007). D63, 1009-1015  [ doi:10.1107/S0907444907037857 ]

Microscale vapour diffusion for protein crystallization

J. Korczynska, T.-C. Hu, D. K. Smith, J. Jenkins, R. Lewis, T. Edwards and A. M. Brzozowski

Synopsis: The development of a new type of vapour-diffusion crystallization plate is reported. It minimizes drop:precipitant volume to an 1:8 ratio and accelerates the rate of crystal growth.

Online 17 August 2007

 

Acta Cryst. (2007). D63, 1016-1021  [ doi:10.1107/S0907444907031319 ]

Effect of a sodium ion on the dehydration-induced phase transition of monoclinic lysozyme crystals

K. Harata and T. Akiba

Synopsis: X-ray diffraction analysis of the dehydration-induced phase transition of monoclinic lysozyme crystals revealed that a sodium ion regulates the structure of the loop region Ser60-Asn74 and intermolecular contacts in the transformed crystal.

PDB references: 2z12, 2z18 and 2z19

Online 17 August 2007

 

Acta Cryst. (2007). D63, 1022-1024  [ doi:10.1107/S0907444907032933 ]

Rapid shape determination of tissue transglutaminase using high-throughput computing

D. Lammie, J. Osborne, D. Aeschlimann and T. J. Wess

Synopsis: This paper discusses the execution of numerous simultaneous runs of the programs DAMMIN and GASBOR using Condor, which distributes them over a network of PCs; this has allowed a substantial acceleration of the processing of results. The application of Condor to determine the molecular shape of tissue transglutaminase is presented, thus demonstrating the efficiency of the approach.

Online 17 August 2007

 

Acta Cryst. (2007). D63, 1025-1028  [ doi:10.1107/S090744490703418X ]

Using barium ions for heavy-atom derivatization and phasing of xylanase II from Trichoderma longibrachiatum

N. Moiseeva and M. Allaire

Synopsis: Barium ions are used to provide phase estimates for xylanase II from T. longibrachiatum by SAD.

Online 17 August 2007