Biological Crystallography

 

Acta Cryst. (2005). D61, 495-504  [ doi:10.1107/S0907444905002350 ]

Structural studies of glucose-6-phosphate and NADP⁺ binding to human glucose-6-phosphate dehydrogenase

M. Kotaka, S. Gover, L. Vandeputte-Rutten, S. W. N. Au, V. M. S. Lam and M. J. Adams

Synopsis: Structures of binary complexes of a human deletion mutant of glucose-6-phosphate dehydrogenase with G6P and with NADP⁺ show substrate and coenzyme binding and confirm the need for a cis proline (172) near the active site. A possible interaction between a second, structural (non-coenzyme) NADP⁺ and the bound G6P is suggested and its implication considered.

PDB references: 2bhl and 2bh9

Online 20 April 2005

 

Acta Cryst. (2005). D61, 505-512  [ doi:10.1107/S0907444905002556 ]

The endoproteinase furin contains two essential Ca²⁺ ions stabilizing its N-terminus and the unique S1 specificity pocket

M. E. Than, S. Henrich, G. P. Bourenkov, H. D. Bartunik, R. Huber and W. Bode

Synopsis: The exact number and the three-dimensional localization of the essential calcium sites within the mammalian prohormone/proprotein convertase furin have been determined by collecting X-ray diffraction data on either side of the Ca  K absorption edge and by calculating a novel type of double difference map from these anomalous scattering data.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 513-519  [ doi:10.1107/S0907444905003070 ]

Crystal engineering yields crystals of cyclophilin D diffracting to 1.7  Å resolution

D. Schlatter, R. Thoma, E. Küng, M. Stihle, F. Müller, E. Borroni, A. Cesura and M. Hennig

Synopsis: It is shown that one single point mutation on the surface of cyclophilin D changed the crystallization properties of the protein to such an extent that crystals of excellent diffraction quality and extreme stability could be obtained.

PDB references: 2bit and 2biu

Online 20 April 2005

 

Acta Cryst. (2005). D61, 520-527  [ doi:10.1107/S0907444905003239 ]

Parameter-space screening: a powerful tool for high-throughput crystal structure determination

Z.-J. Liu, D. Lin, W. Tempel, J. L. Praissman, J. P. Rose and B.-C. Wang

Synopsis: Screening parameter space using a high-throughput pipeline increases the success of protein structure determination.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 528-538  [ doi:10.1107/S0907444905003914 ]

High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability

Y. Eisenberg-Domovich, V. P. Hytönen, M. Wilchek, E. A. Bayer, M. S. Kulomaa and O. Livnah

Synopsis: AVR4 has been crystallized in apo and biotin-complexed forms and their structures have been determined at high resolution.

PDB references: 1y52, 1y53 and 1y55

Online 20 April 2005

 

Acta Cryst. (2005). D61, 539-544  [ doi:10.1107/S0907444905003872 ]

Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam

F. Meilleur, M.-T. Dauvergne, I. Schlichting and D. A. A. Myles

Synopsis: Fully deuterated cytochrome P450cam has been produced and crystallized in order to aid in the determination of its neutron crystallographic structure.

PDB references: 1yrc and 1yrd

Online 20 April 2005

 

Acta Cryst. (2005). D61, 545-555  [ doi:10.1107/S0907444905004038 ]

High-resolution structure of myo-inositol monophosphatase, the putative target of lithium therapy

R. Gill, F. Mohammed, R. Badyal, L. Coates, P. Erskine, D. Thompson, J. Cooper, M. Gore and S. Wood

Synopsis: The structure of myo-inositol monophosphatase, the putative target of lithium therapy for bipolar disorder, has been determined in complex with the physiological magnesium ion ligands. A detailed three-metal mechanism is proposed; the role of the substrate 6-OH group is shown to be in the direct stabilization of the transition state, and mechanisms are proposed for the possible modes of Li⁺ and Mg²⁺ inhibition.

PDB reference: 2bji

Online 20 April 2005

 

Acta Cryst. (2005). D61, 556-565  [ doi:10.1107/S090744490500404X ]

Phasing at resolution higher than the experimental resolution

R. Caliandro, B. Carrozzini, G. L. Cascarano, L. De Caro, C. Giacovazzo and D. Siliqi

Synopsis: The moduli and phases of non-measured reflections are estimated to improve the quality of electron-density maps.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 566-573  [ doi:10.1107/S0907444905004622 ]

COHbC and COHbS crystallize in the R2 quaternary state at neutral pH in the presence of PEG 4000

L. N. Patskovska, Y. V. Patskovsky, S. C. Almo and R. E. Hirsch

Synopsis: COHbC (6K) and COHbS (6V) crystallize in the R2 quaternary form at neutral pH and low ionic strength. These are the first detailed high-resolution R2 quaternary structures reported for human hemoglobins crystallized under conditions approaching physiological.

PDB references: 1m9p and 1nej

Online 20 April 2005

 

Acta Cryst. (2005). D61, 574-579  [ doi:10.1107/S0907444905004804 ]

Preliminary neutron diffraction studies of Escherichia coli dihydrofolate reductase bound to the anticancer drug methotrexate

B. C. Bennett, F. Meilleur, D. A. A. Myles, E. E. Howell and C. G. Dealwis

Synopsis: Neutron diffraction is being used to help determine the positions of H atoms within the active site of DHFR when bound to the inhibitor methotrexate.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 580-588  [ doi:10.1107/S0907444905004889 ]

Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations

J. T. Maynes, M. M. Cherney, M. A. Qasim, M. Laskowski and M. N. G. James

Synopsis: The X-ray crystal structure of subtilisin Carlsberg bound to the broad-specificity protein proteinase inhibitor OMTKY3 reveals two distinct conformations of the inhibitor and rationalizes previous thermodynamic data in terms of additivity.

PDB reference: 1yu6

Online 20 April 2005

 

Acta Cryst. (2005). D61, 589-598  [ doi:10.1107/S0907444905005147 ]

The 2.35  Å structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism

J. Benach, W. C. Edstrom, I. Lee, K. Das, B. Cooper, R. Xiao, J. Liu, B. Rost, T. B. Acton, G. T. Montelione and J. F. Hunt

Synopsis: The structure of the TenA enzyme from P. furiosus is reported with 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate bound at its active site.

PDB reference: 1rtw

Online 20 April 2005

 

Acta Cryst. (2005). D61, 599-604  [ doi:10.1107/S0907444905005512 ]

Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme

M. K. Safo, F. N. Musayev and V. Schirch

Synopsis: The crystal structures of pyridoxine 5'-phosphate oxidase give an insight into the mechanistic pathway of the enzyme.

PDB reference: 1wv4

Online 20 April 2005

 

Acta Cryst. (2005). D61, 605-612  [ doi:10.1107/S0907444905005809 ]

Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark

R. H. G. Baxter, B.-L. Seagle, N. Ponomarenko and J. R. Norris

Synopsis: The structure of the B. viridis reaction center is reported from cryogenic data collection.

PDB reference: 1vrn

Online 20 April 2005

    

Acta Cryst. (2005). D61, 613-621  [ doi:10.1107/S0907444905005743 ]

Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure

T. R. M. Barends, R. M. de Jong, K. E. van Straaten, A.-M.W.H. Thunnissen and B. W. Dijkstra

Synopsis: After phasing a data set with MAD, the crystals were found to be tetartohedrally twinned. A special refinement protocol is described that was established to deal with these data. The resulting structure explains the success of MAD in phasing the data, as well as the reasons for tetartohedral twinning.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 622-627  [ doi:10.1107/S0907444905005895 ]

Structure of human thymidylate synthase under low-salt conditions

L. L. Lovelace, W. Minor and L. Lebioda

Synopsis: The structures of human thymidylate synthase under low-salt conditions and in 2.0  M ammonium sulfate are very similar. The higher resolution obtained enabled the location of a hydrophobic ligand stabilizing the inactive conformation of loop 181-197.

PDB reference: 1ypv

Online 20 April 2005

 

Acta Cryst. (2005). D61, 628-633  [ doi:10.1107/S0907444905007870 ]

Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7  Å resolution: comparison with results from isothermal titration calorimetry

G. H. Cohen, E. W. Silverton, E. A. Padlan, F. Dyda, J. A. Wibbenmeyer, R. C. Willson and D. R. Davies

Synopsis: The structure of the complex between hen egg-white lysozyme and the Fab HyHEL-5 has been re-evaluated at 1.7  Å resolution. The structural results have been compared with the results of isothermal titration calorimetry.

PDB reference: 1yqv

Online 20 April 2005

 

Acta Cryst. (2005). D61, 634-636  [ doi:10.1107/S0907444905005883 ]

SSEP-2.0: Secondary Structural Elements of Proteins

B. Balamurugan, K. Samaya Mohan, J. Ramesh, M. N. A. Md. Roshan, K. Sumathi and K. Sekar

Synopsis: The Secondary Structural Elements of Proteins (SSEP) database is an integrated and comprehensive knowledge base for accessing information related to all the secondary-structural elements present in non-redundant (25 and 90%) protein chains. The new version 2.0 is described here.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 637-639  [ doi:10.1107/S0907444905005871 ]

CADB-2.0: Conformation Angles Database

K. Samaya Mohan, S. S. Sheik, J. Ramesh, B. Balamurugan, M. Jeyasimhan, C. Mayilarasi and K. Sekar

Synopsis: The Conformation Angles Data Base (CADB) is a comprehensive, authoritative and timely knowledge base with a powerful query engine developed to facilitate the retrieval of information related to the conformational angles (main chain and side chain) of the amino-acid residues present in non-redundant (both 25 and 90%) data sets. An updated version is decribed here..

Online 20 April 2005

 

Acta Cryst. (2005). D61, 640-642  [ doi:10.1107/S090744490500541X ]

A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans

N. Sukumar, P. Langan, F. S. Mathews, L. H. Jones, P. Thiyagarajan, B. P. Schoenborn and V. L. Davidson

Synopsis: Crystals of the blue copper protein amicyanin of dimensions 2 × 1.3 × 1  mm, crystallized and macroseeded repeatedly using solutions made in D₂O throughout the crystal-growth process, diffracted neutrons to a resolution of 1.9  Å.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 643-645  [ doi:10.1107/S0907444905007262 ]

Sample preparation and mass-spectrometric characterization of crystal-derived protein samples

J. E. Nettleship, T. S. Walter, R. Aplin, D. K. Stammers and R. J. Owens

Synopsis: A method is described for preparing crystals for mass spectrometry. An example of its use is given.

Online 20 April 2005

 

Acta Cryst. (2005). D61, 646-650  [ doi:10.1107/S0907444905007924 ]

Crystallization of foot-and-mouth disease virus 3C protease: surface mutagenesis and a novel crystal-optimization strategy

J. R. Birtley and S. Curry

Synopsis: A soluble recombinant form of the 3C protease from foot-and-mouth disease virus was produced by substitution of two surface-exposed cysteines. Crystals that diffract to high resolution (1.9  Å) were obtained with a simple optimization strategy using standard screening solutions.

Online 20 April 2005