Biological Crystallography

 

Acta Cryst. (2005). D61, 1013-1021  [ doi:10.1107/S0907444905012734 ]

Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method

Y. Kitago, N. Watanabe and I. Tanaka

Synopsis: A novel protein structure was solved by S-SAD using in-house chromium radiation. To reduce the X-ray absorption of the cryo-buffer and cryoloop, a novel free crystal-mounting technique was developed.

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1022-1030  [ doi:10.1107/S0907444905012989 ]

Getting the most out of X-ray home sources

R. A. P. Nagem, A. L. B. Ambrosio, A. L. Rojas, M. V. A. S. Navarro, A. M. Golubev, R. C. Garratt and I. Polikarpov

Synopsis: A 14 kDa phospholipase, an 18 kDa proteinase inhibitor and a novel 60 kDa glycoside hydrolase were crystallized and their three-dimensional structures were determined using diffraction data collected using a copper rotating-anode X-ray source. Experimental phases were obtained from the anomalous signal provided by S atoms in the case of phospholipase and by I atoms rapidly incorporated into the native structure using the quick cryo-soaking approach in the latter two cases.

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1031-1040  [ doi:10.1107/S0907444905013090 ]

High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide

T. Blicher, J. S. Kastrup, S. Buus and M. Gajhede

Synopsis: This paper describes the 1.45 Å structure of the human MHC-I molecule HLA-A*1101 in complex with a peptide derived from the SARS coronavirus N protein. Implications for vaccine design are discussed.

PDB reference: 1x7q

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1041-1048  [ doi:10.1107/S0907444905013806 ]

A modified vapor-diffusion crystallization protocol that uses a common dehydrating agent

K. V. Dunlop and B. Hazes

Synopsis: The shared reservoir solution method, a vapor-diffusion crystallization method where many different experiments share the same reservoir solution, is described.

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1049-1056  [ doi:10.1107/S090744490501382X ]

Structure of the uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans

I. Leiros, E. Moe, A. O. Smalås and S. McSweeney

Synopsis: The three-dimensional structure of uracil-DNA N-glycosylase (UNG) from D. radiodurans has been determined to a resolution of 1.8 Å. An increased number of positively charged residues in the DNA-binding region suggest an explanation of the observed improvement in substrate binding.

PDB reference: 2boo

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1057-1066  [ doi:10.1107/S0907444905013831 ]

De novo calcium/sulfur SAD phasing of the human formylglycine-generating enzyme using in-house data

D. Roeser, A. Dickmanns, K. Gasow and M. G. Rudolph

Synopsis: Orthorhombic crystals of the human formylglycine-generating enzyme were grown and phased using SAD based on the anomalous signal of Ca²⁺ and sulfur using data collected on a rotating-anode generator at the Cu K wavelength of 1.54 Å.

PDB reference: 1z70

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1067-1071  [ doi:10.1107/S0907444905014162 ]

Structure of myelin P2 protein from equine spinal cord

D. J. B. Hunter, R. Macmaster, A. W. Roszak, A. Riboldi-Tunnicliffe, I. R. Griffiths and A. A. Freer

Synopsis: As an initial characterization of myelin proteins from equine tissue we have purified and crystallized equine P2 from CNS myelin under detergent conditions. The structure was solved to 2.1 Å and shows a molecule of HEPES and the detergent LDAO in the binding cavity.

PDB reference: 1yiv

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1072-1079  [ doi:10.1107/S0907444905014356 ]

Structure of the wild-type TEM-1 -lactamase at 1.55 Å and the mutant enzyme Ser70Ala at 2.1 Å suggest the mode of noncovalent catalysis for the mutant enzyme

B. Stec, K. M. Holtz, C. L. Wojciechowski and E. R. Kantrowitz

Synopsis: The structure of the wild-type TEM-1 at 1.55 Å and the mutant enzyme Ser70Ala at 2.1 Å resolution are presented. The structures suggest the noncovalent mode of catalysis for the mutant enzyme.

PDB references: 1zg4 and 1zg6

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1080-1087  [ doi:10.1107/S0907444905015519 ]

Ab initio phasing at resolution higher than 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 extrapolated to facilitate the ab initio phasing of macromolecules.

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1088-1098  [ doi:10.1107/S0907444905015581 ]

The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique

T. Chatake, I. Tanaka, H. Umino, S. Arai and N. Niimura

Synopsis: A single-crystal neutron diffraction study has been carried out at 1.8 Å resolution on the Z-DNA hexamer d(CGCGCG).

PDB references: 1v9g and 1woe

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1099-1106  [ doi:10.1107/S0907444905015866 ]

Ab initio crystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell

J. Taka, H. Naitow, M. Yoshimura, N. Miyazaki, A. Nakagawa and T. Tsukihara

Synopsis: An ab initio method was effectively applied to determine the crystal structures of spherical viruses that are uniquely located at centrosymmetric positions in unit cells.

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1107-1115  [ doi:10.1107/S0907444905016069 ]

Structure of the zinc-saturated C-terminal lobe of bovine lactoferrin at 2.0 Å resolution

T. Jabeen, S. Sharma, N. Singh, A. Bhushan and T. P. Singh

Synopsis: The C-terminal lobe of bovine lactoferrin was prepared proteolytically using proteinase K. The binding studies with metal ions indicate that a zinc ion remains bound to the C-terminal lobe at pH up to 3.8. The structure of the zinc-saturated C-terminal lobe shows that Zn²⁺ is bound in the metal-binding cleft with octahedral coordination.

PDB reference: 1sdx

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1116-1124  [ doi:10.1107/S0907444905016318 ]

The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance

R. C. J. Dobson, M. D. W. Griffin, G. B. Jameson and J. A. Gerrard

Synopsis: The crystal structures at resolutions better than 2.0 Å of native and (S)-lysine-bound dihydrodipicolinate synthase from E. coli are presented and analysed.

PDB references: 1yxc and 1yxd

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1125-1131  [ doi:10.1107/S0907444905016781 ]

Structure of d(TGCGCG)·d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA

S. Thiyagarajan, S. S. Rajan and N. Gautham

Synopsis: The sequence d(TGCGCG)·d(CGCGCA) crystallized in two crystal forms. The structures have been solved in space groups P2₁2₁2₁ and P6₅. The effects of sequence and crystal packing on the structure are reported.

NDB references: ZD0013 and ZD0014

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1132-1139  [ doi:10.1107/S0907444905016732 ]

Extraction of functional motion in trypsin crystal structures

A. Schmidt and V. S. Lamzin

Synopsis: Extraction and visualization of functionally relevant directional motion from the anisotropic atomic displacement parameters in a series of trypsin structures are described.

PDB references: 1xvm and 1xvo

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1140-1148  [ doi:10.1107/S0907444905016896 ]

Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association

K. Saikrishnan, G. P. Manjunath, P. Singh, J. Jeyakanthan, Z. Dauter, K. Sekar, K. Muniyappa and M. Vijayan

Synopsis: Structural analysis of the single-stranded DNA-binding protein (SSB) from M. smegmatis and related studies confirm the clamp arrangement that stabilizes the dimer and the ellipsoidal shape of the tetramer to be characteristic features of mycobacterial SSBs. Proteins from different sources exhibit considerable variability in quaternary association.

PDB references: 1x3e, 1x3f and 1x3g

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1149-1159  [ doi:10.1107/S0907444905017038 ]

Impact of natural variation in bacterial F17G adhesins on crystallization behaviour

L. Buts, A. Wellens, I. Van Molle, L. Wyns, R. Loris, M. Lahmann, S. Oscarson, H. De Greve and J. Bouckaert

Synopsis: The rate of successful crystallization of prokaryotic proteins can be readily enhanced by utilizing natural intraspecies variants. This is exemplified by the crystallization of six known variants of the lectin domain of the F17G fimbrial adhesin and the analysis of the compatibilities of their sequences with the obtained crystal forms.

PDB references: 2bsc, 1zpl, 2bs7, 2bs8, 2bsb and 1zk5

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1160-1164  [ doi:10.1107/S0907444905017270 ]

Structure of the lipopeptide antibiotic tsushimycin

G. Bunkóczi, L. Vértesy and G. M. Sheldrick

Synopsis: The daptomycin relative tsushimycin is one of the largest structures solved by ab initio direct methods and provides the first X-ray structure for this antibiotic class.

PDB reference: 1w3m

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1165-1171  [ doi:10.1107/S0907444905017336 ]

A nanovolume crystallization robot that creates its crystallization screens on-the-fly

B. Hazes and L. Price

Synopsis: The use of a nanovolume asynchronous crystallization robot both to create combinatorial crystallization screens and to set up the crystallization experiments is described.

Online 20 July 2005

 

Acta Cryst. (2005). D61, 1172  [ doi:10.1107/S0907444905013533 ]

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

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

Synopsis: An addendum and erratum to the paper by Barends et al. (2005), Acta Cryst. D61, 613-621.

Online 20 July 2005