Biological Crystallography

 

Acta Cryst. (2005). D61, 355-364  [ doi:10.1107/S090744490403389X ]

Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug target

K. A. Kantardjieff, C. Vasquez, P. Castro, N. M. Warfel, B.-S. Rho, T. Lekin, C.-Y. Kim, B. W. Segelke, T. C. Terwilliger and B. Rupp

Synopsis: The 1.9  Å native structure of the pyrimidine-biosynthesis regulatory protein encoded by the M. tuberculosis pyrR gene (Rv1379) is reported. Because pyrimidine biosynthesis is an essential step in the progression of TB, pyrR is an attractive antitubercular drug target.

PDB reference: 1w30

Online 24 March 2005

 

Acta Cryst. (2005). D61, 365-373  [ doi:10.1107/S0907444904033876 ]

Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose

N. M. Koropatkin and H. M. Holden

Synopsis: The structure of CDP-D-glucose 4,6-dehydratase from S. typhi complexed with CDP-D-xylose has been determined to 1.8  Å resolution.

PDB reference: 1wvg

Online 24 March 2005

 

Acta Cryst. (2005). D61, 374-379  [ doi:10.1107/S0907444904034390 ]

Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4  Å resolution

A. Philippsen, T. Schirmer, M. A. Stein, F. Giffhorn and J. Stetefeld

Synopsis: This paper reports the first atomic structure of a bacterial sorbitol dehydrogenase, with a model of the active site containing the cofactor NAD and the substate sorbitol.

PDB references: 1k2w and 1uzo

Online 24 March 2005

 

Acta Cryst. (2005). D61, 380-387  [ doi:10.1107/S0907444905000181 ]

Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0  Å

L. Huang, T. M. Borders, J. T. Shen, C.-J. Wang and E. A. Berry

Synopsis: A multi-subunit mitochondrial membrane-protein complex involved in the Krebs cycle and respiratory chain has been crystallized in a form suitable for near-atomic resolution structure determination.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 388-396  [ doi:10.1107/S0907444905000429 ]

Automatic structure determination based on the single-wavelength anomalous diffraction technique away from an absorption edge

G. A. Leonard, G. Sainz, M. M. E. de Backer and S. McSweeney

Synopsis: The routine use of the single-wavelength anomalous diffraction technique (SAD) at wavelengths remote from absorption edges as a method for automated structure determination is discussed.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 397-406  [ doi:10.1107/S0907444905000417 ]

Structure of a liganded type 2 non-specific lipid-transfer protein from wheat and the molecular basis of lipid binding

F. Hoh, J.-L. Pons, M.-F. Gautier, F. de Lamotte and C. Dumas

Synopsis: The crystal structure of wheat ns-LTP2 was determined ab initio to 1.12  Å resolution by direct methods. The -helical bundle fold of this protein is maintained by four disulfide bridges and delineates two hydrophobic cavities filled by the alkyl chains of lipids.

PDB reference: 1tuk

Online 24 March 2005

 

Acta Cryst. (2005). D61, 407-415  [ doi:10.1107/S090744490500082X ]

Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

E. Alexopoulos, E. A. Jares-Erijman, T. M. Jovin, R. Klement, R. Machinek, G. M. Sheldrick and I. Usón

Synopsis: In the crystal, actinomycin D intercalates between G-T wobble pairs of DNA involving the sequence d(TTAGTT); in solution, the dominant binding is between guanine and actinomycin.

PDB references: 1unm and 1unj

Online 24 March 2005

 

Acta Cryst. (2005). D61, 416-422  [ doi:10.1107/S0907444905001216 ]

Combined use of AFM and X-ray diffraction to analyze crystals of an engineered, domain-deleted antibody

S. B. Larson, Y. G. Kuznetsov, J. Day, J. Zhou, S. Glaser, G. Braslawsky and A. McPherson

Synopsis: A human-mouse chimeric antibody lacking any C_H2 domain has been crystallized for diffraction analysis in the presence of detergent. Analysis by atomic force microscopy reveals the symmetry properties of the asymmetric unit and the presence of an unusual kind of defect within the crystals.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 423-432  [ doi:10.1107/S0907444905001393 ]

Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme

I. Margiolaki, J. P. Wright, A. N. Fitch, G. C. Fox and R. B. Von Dreele

Synopsis: Powder diffraction data are shown to be sufficient to position a molecule of turkey egg-white lysozyme in the hexagonal unit cell by molecular replacement and to refine the structure at 3.35  Å resolution. The variation of the structure with sample preparation and upon freezing are also reported.

PDB reference: 1xft

Online 24 March 2005

 

Acta Cryst. (2005). D61, 433-441  [ doi:10.1107/S0907444905000399 ]

Structure of gramicidin D-RbCl complex at atomic resolution from low-temperature synchrotron data: interactions of double-stranded gramicidin channel contents and cations with channel wall

M. L. Glówka, A. Olczak, J. Bojarska, M. Szczesio, W. L. Duax, B. M. Burkhart, W. A. Pangborn, D. A. Langs and Z. Wawrzak

Synopsis: A 1.14  Å resolution study on the gramicidin D complex with RbCl confirms its right-handed antiparallel double-stranded dimeric structure. Rb cations distributed over seven binding sites in each gramicidin channel unit are `coordinated' by delocalized -electrons of three to five carbonyl groups from the channel wall and by two water molecules.

PDB reference: 1w5u

Online 24 March 2005

 

Acta Cryst. (2005). D61, 442-448  [ doi:10.1107/S090744490500137X ]

Structures of complexes between echinomycin and duplex DNA

J. A. Cuesta-Seijo and G. M. Sheldrick

Synopsis: The classical bis-intercalation complexes of echinomycin with DNA have been examined at high resolution.

PDB references: 1pfe, 1xvk, 1xvr and 1xvn

Online 24 March 2005

 

Acta Cryst. (2005). D61, 449-457  [ doi:10.1107/S0907444905001307 ]

Auto-Rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment

S. Panjikar, V. Parthasarathy, V. S. Lamzin, M. S. Weiss and P. A. Tucker

Synopsis: A description of the EMBL-Hamburg Automated Crystal Structure Determination Platform is given and examples of successful structure determination are presented.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 458-464  [ doi:10.1107/S0907444905001617 ]

Likelihood-enhanced fast translation functions

A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni and R. J. Read

Synopsis: Derivation of likelihood-enhanced translation functions that can be calculated by fast Fourier transform.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 465-471  [ doi:10.1107/S0907444905001897 ]

A molecular viewer for the analysis of TLS rigid-body motion in macromolecules

J. Painter and E. A. Merritt

Synopsis: TLSView is an interactive molecular viewer for the generation, visualization and analysis of TLS (translation/libration/screw) models of protein motion.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 472-476  [ doi:10.1107/S0907444905003331 ]

Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-dependent catalytic antibody

B. Golinelli-Pimpaneau

Synopsis: The structure of a pyridoxal phosphate-dependent catalytic antibody in complex with a substrate analogue has been determined from a monoclinic pseudomerohedrally twinned crystal. Iodide molecules are present in the combining site and at intermolecular contacts.

PDB reference: 1wc7

Online 24 March 2005

 

Acta Cryst. (2005). D61, 477-480  [ doi:10.1107/S0907444905001204 ]

Favourable mediation of crystal contacts by cocoamidopropylbetaine (CAPB)

S. Özbek, J. F. Müller, E. Figgemeier and J. Stetefeld

Synopsis: A novel approach for optimizing crystal contacts in a most favourable fashion by performing crystallization setups with the zwitterionic surfactant cocoamidoproylbetaine (CAPB) is introduced.

PDB reference: 1ybk

Online 24 March 2005

 

Acta Cryst. (2005). D61, 481-484  [ doi:10.1107/S0907444905001502 ]

Structure of S35C flavodoxin mutant from Desulfovibrio vulgaris in the semiquinone state

R. Artali, N. Marchini, F. Meneghetti, D. Cavazzini, A. Cassetta and C. Sassone

Synopsis: The crystal structure of the S35C flavodoxin from D. vulgaris in the semiquinone state at 1.8  Å resolution. shows as main difference with the oxidized form a conformational change of the carbonyl oxygen of Gly61, leading to the formation of a new hydrogen bond between the protein and the prosthetic group.

PDB reference: 1xt6

Online 24 March 2005

 

Acta Cryst. (2005). D61, 485-489  [ doi:10.1107/S0907444905000910 ]

Unusual non-crystallographic symmetry in crystals of a 420  kDa crustacean clottable protein

J. M. Kollman and R. F. Doolittle

Synopsis: The clottable protein from the California spiny lobster has been purified and crystallized in two forms. One of the crystal forms exhibits unusual pseudo-ninefold rotational symmetry in space group P2₁.

Online 24 March 2005

 

Acta Cryst. (2005). D61, 490-493  [ doi:10.1107/S0907444905002726 ]

Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments

J. Newman

Synopsis: Equilibrating crystallization drops against different reservoirs can alter the results of a vapor-diffusion crystallization experiment.

Online 24 March 2005