Biological Crystallography

 

Acta Cryst. (2006). D62, 687-694  [ doi:10.1107/S0907444906014727 ]

Solution of protein crystallographic structures by high-pressure cryocooling and noble-gas phasing

C. U. Kim, Q. Hao and S. M. Gruner

Synopsis: A method has been developed for readily preparing crystals for noble-gas SAD phasing and cryopreservation and has been demonstrated with the 240-residue 26 kDa protein porcine pancreas elastase (PPE). The diffraction quality of the method is sufficiently high that a single 0.31 occupied krypton site was sufficient for SAD phasing at 1.3 Å resolution.

Online 20 June 2006

 

Acta Cryst. (2006). D62, 695-706  [ doi:10.1107/S0907444906014764 ]

High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D₂-symmetric active site

N. Narayana

Synopsis: The first high-resolution structure (1.1 Å resolution) of a trimethoprim-resistant plasmid-encoded R67 DHFR is described. Sheets of pentagonal networks of water molecules in the D₂-symmetric active site may play a role in ligand binding, catalysis and inhibition.

PDB reference: 2gqv

Online 20 June 2006

 

Acta Cryst. (2006). D62, 707-716  [ doi:10.1107/S0907444906014946 ]

In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs

G. N. Sarma and P. A. Karplus

Synopsis: Sulfur SAD data analyses reveal that successful substructure solution and phasing is a sensitive function of choices made regarding the length of data collection and resolution cutoffs.

Online 20 June 2006

 

Acta Cryst. (2006). D62, 717-724  [ doi:10.1107/S0907444906014855 ]

Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A₂

K. Sekar, M. Yogavel, S. P. Kanaujia, A. Sharma, D. Velmurugan, M.-J. Poi, Z. Dauter and M.-D. Tsai

Synopsis: The paper reports two forms of the crystal structure of a quadruple mutant (K53,56,120,121M) of PLA₂. The two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA₂ at the lipid interface and in solution, respectively.

PDB references: 2bd1 and 2bch

Online 20 June 2006

 

Acta Cryst. (2006). D62, 725-733  [ doi:10.1107/S0907444906015319 ]

The structure of human neuronal Rab6B in the active and inactive form

I. Garcia-Saez, S. Tcherniuk and F. Kozielski

Synopsis: The crystal structure of the human Rab protein Rab6B in its inactive (with bound MgGDP) and active (MgGTPS-bound) forms have been determined to 2.3 and 1.8 Å, respectively. Both crystallized in space group P2₁2₁2₁, with similar unit-cell parameters.

PDB references: 2fe4 and 2ffq

Online 20 June 2006

 

Acta Cryst. (2006). D62, 734-740  [ doi:10.1107/S0907444906015824 ]

Determination of the crystal structure of EntA, a 2,3-dihydro-2,3-dihydroxybenzoic acid dehydrogenase from Escherichia coli

J. A. Sundlov, J. A. Garringer, J. M. Carney, A. S. Reger, E. J. Drake, W. L. Duax and A. M. Gulick

Synopsis: The structure of the E. coli EntA protein, a bacterial member of the short-chain oxidoreductase family of enzymes, has been solved at 2.0 Å. Analysis of core residues from other family members allows the identification of active-site residues.

PDB reference: 2fwm

Online 20 June 2006

 

Acta Cryst. (2006). D62, 741-749  [ doi:10.1107/S0907444906016076 ]

Automated ligand placement and refinement with a combined force field and shape potential

S. Wlodek, A. G. Skillman and A. Nicholls

Synopsis: An automated computational procedure for fitting a ligand into its electron density with the use of the MMFF94 force field and a Gaussian shape description has been developed.

Online 20 June 2006

 

Acta Cryst. (2006). D62, 750-765  [ doi:10.1107/S0907444906016222 ]

Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p

R. C. Hillig and L. Renault

Synopsis: This case study shows that partial merohedral twinning does not hinder MIR phasing if it is recognized and the phasing and refinement procedures are adjusted accordingly. Identification of hemihedral twinning, twin correction and different refinement strategies for twinned data are discussed.

PDB reference: 2ca6

Online 20 June 2006

 

Acta Cryst. (2006). D62, 766-775  [ doi:10.1107/S0907444906016982 ]

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 Å resolution

E. Skrzypczak-Jankun, O. Y. Borbulevych, M. I. Zavodszky, M. R. Baranski, K. Padmanabhan, V. Petricek and J. Jankun

Synopsis: Flash-freezing and/or ligand binding can cause changes not only in crystal packing but also in the size and shape of the internal cavities in the protein molecule.

PDB references: 1rrh and 1rrl

Online 20 June 2006

 

Acta Cryst. (2006). D62, 776-783  [ doi:10.1107/S0907444906017318 ]

Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin

R. Aranda, E. J. Levin, F. Schotte, P. A. Anfinrud and G. N. Phillips

Synopsis: X-ray crystal structures of transient intermediate states after the photolysis of carbon monoxide from myoglobin reveal a non-linear progression toward the deoxy state.

PDB references: 2g0r, 2g0s, 2g0v, 2g0x, 2g0z, 2g10, 2g11, 2g12 and 2g14

Online 20 June 2006

 

Acta Cryst. (2006). D62, 784-792  [ doi:10.1107/S0907444906017379 ]

Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement

N. Watanabe, T. Akiba, R. Kanai and K. Harata

Synopsis: The crystal structure of an orthorhombic form of xylanase II was determined at atomic resolution and its structural fluctuation was evaluated by analyzing the anisotropic displacement parameters.

PDB references: 2dfb and 2dfc

Online 20 June 2006

 

Acta Cryst. (2006). D62, 793-799  [ doi:10.1107/S0907444906017537 ]

Structure of the C2A domain of rabphilin-3A

M. Biadene, P. Montaville, G. M. Sheldrick and S. Becker

Synopsis: The first crystal structure of a C2 domain of rabphilin-3A is reported.

PDB reference: 2chd

Online 20 June 2006

 

Acta Cryst. (2006). D62, 800-806  [ doi:10.1107/S0907444906018294 ]

Structure of human ferritin L chain

Z. Wang, C. Li, M. Ellenburg, E. Soistman, J. Ruble, B. Wright, J. X. Ho and D. C. Carter

Synopsis: High-resolution X-ray structures of human ferritin L chain in two different crystal forms revealed new insights in the mechanism of iron storage.

Online 20 June 2006

 

Acta Cryst. (2006). D62, 807-813  [ doi:10.1107/S0907444906019196 ]

The 1.9 Å resolution structure of Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase, a potential drug target

L. M. Henriksson, C. Björkelid, S. L. Mowbray and T. Unge

Synopsis: The crystal structure of M. tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase, with a sulfate bound in the expected site of the phosphate moiety of the sugar substrate, has been determined to 1.9 Å resolution. Structure and sequence comparisons offer suggestions for the design of specific drugs.

PDB reference: 2c82

Online 20 June 2006

 

Acta Cryst. (2006). D62, 814-823  [ doi:10.1107/S0907444906019895 ]

Structure of Escherichia coli tryptophanase

S.-Y. Ku, P. Yip and P. L. Howell

Synopsis: The structure of the apo form of the enzyme with sulfate ions bound in the active site is presented. The structure is in a `closed' conformation relative to structures of the P. vulgaris enzyme.

PDB reference: 2c44

Online 20 June 2006

 

Acta Cryst. (2006). D62, 824-832  [ doi:10.1107/S090744490601804X ]

Structure of 8S globulin, the major seed storage protein of mung bean

T. Itoh, R. N. Garcia, M. Adachi, Y. Maruyama, E. M. Tecson-Mendoza, B. Mikami and S. Utsumi

Synopsis: The crystal structure of 8S globulin of mung bean was determined at 2.65 Å resolution and its physicochemical properties were elucidated in comparison with other seed storage globulins.

PDB reference: 2cv6

Online 20 June 2006

 

Acta Cryst. (2006). D62, 833-842  [ doi:10.1107/S0907444906018385 ]

Assessment of a preliminary solubility screen to improve crystallization trials: uncoupling crystal condition searches

A. Izaac, C. A. Schall and T. C. Mueser

Synopsis: A preliminary screen has been used to maximize solubility and define buffer and salt conditions for optimal protein crystal growth of ten test proteins. A precipitant/precipitant-additive screen is also presented which is used in conjunction with the preliminary screen to define a two-step approach to crystal screening.

Online 20 June 2006