Biological Crystallography

 

Acta Cryst. (2003). D59, 619  [ doi:10.1107/S0907444903005900 ]

DNA and beyond

E. N. Baker and Z. Dauter

Online 25 March 2003

 

Acta Cryst. (2003). D59, 620-626  [ doi:10.1107/S0907444903003251 ]

A glossary of DNA structures from A to Z

A. Ghosh and M. Bansal

Synopsis: This review provides a glossary of currently identified DNA structures and outlines the present understanding of DNA structure exactly 50 years after the original discovery of the structure of DNA by Watson and Crick. It also highlights the need for caution when assigning names to novel DNA polymorphs.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 627-636  [ doi:10.1107/S0907444903001227 ]

Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching

A. J. Oakley, T. Heinrich, C. A. Thompson and M. C. J. Wilce

Synopsis: The structure of a thermostable family 11 xylanase from B. subtilis subspecies B230 is presented and the structure analysed. Possible means of improving the thermostability of this enzyme are suggested.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 637-643  [ doi:10.1107/S0907444903001938 ]

The catalytic module of Cel7D from Phanerochaete chrysosporium as a chiral selector: structural studies of its complex with the beta blocker (R)-propranolol

I. G. Muñoz, S. L. Mowbray and J. Ståhlberg

Synopsis: The 1.5  Å structure of the catalytic domain of the major cellulase of P. chrysosporium, Cel7D (CBH 58), gives new insights into the basis of enantioselectivity in this family of enzymes.

PDB reference: 1h46

Online 25 March 2003

 

Acta Cryst. (2003). D59, 644-653  [ doi:10.1107/S090744490300194X ]

Structure of dimeric cytochrome c₃ from Desulfovibrio gigas at 1.2  Å resolution

D. Aragão, C. Frazão, L. Sieker, G. M. Sheldrick, J. LeGall and M. A. Carrondo

Synopsis: High-resolution refinement of dimeric cytochrome c₃ and detailed sequence and structural comparison with all other known c₃ domains are described.

PDB reference: 1gyo

Online 25 March 2003

 

Acta Cryst. (2003). D59, 654-661  [ doi:10.1107/S0907444903001951 ]

Analysis of two polymorphic forms of a pyrido[2,3-d]pyrimidine N9-C10 reversed-bridge antifolate binary complex with human dihydrofolate reductase

V. Cody, N. Galitsky, J. R. Luft, W. A. Pangborn and A. Gangjee

Synopsis: The structure determination of human dihydrofolate reductase as a binary complex with the potent N9-C10 reversed-bridge antifolate inhibitor 2,4-diamino-6-[N-(3',4',5'-trimethoxybenzyl)-N-methylamino]pyrido[2,3-d]pyrimidine is reported for two independent polymorphic rhombohedral R3 lattices.

PDB references: 1mvs and 1mvt

Online 25 March 2003

 

Acta Cryst. (2003). D59, 662-669  [ doi:10.1107/S0907444903002129 ]

SAD or MAD phasing: location of the anomalous scatterers

M. C. Burla, B. Carrozzini, G. L. Cascarano, C. Giacovazzo and G. Polidori

Synopsis: A procedure is described for locating the anomalous scatterers in SAD and MAD cases.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 670-676  [ doi:10.1107/S0907444903002208 ]

Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding

J. Diao

Synopsis: The occupancy change of the double conformation of GluB13 characterizes a pH-dependent dynamic switching process. The occupancy of the sulfate ion decreases as the pH increases. Comparisons of the observed structure factors and structures indicate that the porcine insulin structure changes gradually as a function of pH.

PDB references: 1b17, 1b18, 1b19, 1b2a, 1b2b, 1b2c, 1b2d, 1b2e, 1b2f and 1b2g

Online 25 March 2003

 

Acta Cryst. (2003). D59, 677-687  [ doi:10.1107/S0907444903002233 ]

1.3  Å X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization

L.-O. Essen, A. Harrenga, C. Ostermeier and H. Michel

Synopsis: The structure of the antibody Fv fragment 7E2 that is directed against the cytochrome c oxidase from Paracoccus denitrificans shows that variable domains have highly conserved solvent shells along their framework regions. The structure reveals local `breathing' inside the hydrophobic cores, a novel CDR-L3 loop conformation and peculiar differences in the V_H/V_L-pairing.

PDB reference: 1mqk

Online 25 March 2003

 

Acta Cryst. (2003). D59, 688-696  [ doi:10.1107/S0907444903002646 ]

In-house measurement of the sulfur anomalous signal and its use for phasing

J. É. Debreczeni, G. Bunkóczi, Q. Ma, H. Blaser and G. M. Sheldrick

Synopsis: SAD phasing based primarily on sulfur anomalous scattering measured in-house led to easily interpretable maps for five standard test proteins.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 697-708  [ doi:10.1107/S0907444903002713 ]

Heat transfer from protein crystals: implications for flash-cooling and X-ray beam heating

S. Kriminski, M. Kazmierczak and R. E. Thorne

Synopsis: An analysis of heat transfer from protein crystals is used to prioritize experimental parameters affecting the success of low-temperature X-ray data-collection procedures and to evaluate methods for reducing crystal heating by X-ray absorption.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 709-718  [ doi:10.1107/S0907444903002889 ]

Structure determination of a small protein through a 23-dimensional molecular-replacement search

N. M. Glykos and M. Kokkinidis

Synopsis: A stochastic multidimensional molecular-replacement method has successfully been applied to a 23-dimensional problem.

PDB reference: 1gmg

Online 25 March 2003

 

Acta Cryst. (2003). D59, 719-720  [ doi:10.1107/S0907444902022527 ]

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of HP1352, a putative DNA methyltransferase in Helicobacter pylori

K. Schirwitz, A. Lundin, A. Skoglund, M. Krabbe, L. Engstrand and C. Enroth

Synopsis: Crystals of the DNA methyltransferase HP1352 from H. pylori have been obtained and diffract to 2.5  Å resolution.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 721-723  [ doi:10.1107/S0907444903001987 ]

Crystallization and preliminary X-ray data of the ₂₂ subcomponent of the acetyl-CoA decarbonylase/synthase multienzyme complex from Methanosarcina thermophila

P. Balbo and M. Oliveira

Synopsis: The Ni/Fe-S-dependent ₂₂ subcomponent of the acetyl-CoA decarbonylase/synthase from M. thermophila was purified and crystallized. The crystals were mounted in a capillary and diffracted to 4.0  Å resolution at room temperature using a synchrotron-radiation source.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 724-726  [ doi:10.1107/S0907444903002063 ]

Crystallization of the actin-binding domain of human -actinin: analysis of microcrystals of SeMet-labelled protein

F. Ekström, G. Stier and U. H. Sauer

Synopsis: The actin-binding domain of human -actinin has been cloned, expressed and crystallized. Single-wavelength anomalous dispersion data were collected from microcrystals of selenomethionine-labelled protein using a microfocused synchrotron X-ray beam.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 727-729  [ doi:10.1107/S0907444903002117 ]

Crystallization and preliminary X-ray data of amine oxidase from bovine serum

V. Calderone, M. L. Di Paolo, M. Trabucco, M. Biadene, R. Battistutta, A. Rigo and G. Zanotti

Synopsis: The copper-containing amine oxidase from bovine serum (BSAO) has been deglycosylated and crystallized. Crystals belong to space group P2₁2₁2₁, with a dimer in the asymmetric unit.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 730-733  [ doi:10.1107/S0907444903002191 ]

Purification, crystallization and preliminary crystallographic analysis of AHP IX-bp, a zinc ion and pH-dependent coagulation factor IX binding protein from Agkistrodon halys Pallas venom

J. Zang, M. Teng and L. Niu

Synopsis: AHP IX-bp, a new coagulation factor IX binding protein, was purified from the venom of A. halys Pallas and its biochemical properties were partially characterized. The crystals of AHP IX-bp at two different pH conditions were obtained and the X-ray diffraction data were collected and reduced respectively.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 734-736  [ doi:10.1107/S0907444903002245 ]

Purification, crystallization and preliminary X-ray analysis of ferredoxin isolated from thermophilic cyanobacterium Mastigocladus laminosus

A. Fish, M. Lebendiker, R. Nechushtai and O. Livnah

Synopsis: Ferredoxin obtained from M. laminosus has been purified and crystallized. The future-determined crystal structure is expected to provide valuable data on the factors inducing thermostability in proteins.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 737-740  [ doi:10.1107/S0907444903002671 ]

Purification, crystallization and preliminary X-ray analysis of two nudix hydrolases from Deinococcus radiodurans

E. L. Holbrook, U. Schulze-Gahmen, G. W. Buchko, S. Ni, M. A. Kennedy and S. R. Holbrook

Synopsis: Two putative nudix hydrolases, DR1025 and DR0079, from the radioresistant bacterium D. radiodurans have been expressed, purified, crystallized and their diffraction data collected to 1.4 and 1.9  Å resolution, respectively. Anomalous diffraction data were measured to 1.8  Å resolution for an Sm³⁺ derivative of DR1025.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 741-743  [ doi:10.1107/S0907444903002634 ]

Crystallization and preliminary X-ray analysis of native and selenomethionine 2-hydroxybiphenyl 3-monooxygenase

A. Meyer, D. Tanner, A. Schmid, D. F. Sargent, H.-P.E. Kohler and B. Witholt

Synopsis: 2-Hydroxybiphenyl 3-monooxygenase (HbpA) from P. azelaica HBP1 was crystallized as both native and selenomethionine-labelled protein (SeMet HbpA). From these crystals, diffraction data were collected to a resolution of 2.0  Å for native and 2.25  Å for SeMet HbpA.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 744-746  [ doi:10.1107/S0907444903002890 ]

Crystallization and preliminary X-ray diffraction study of a wheat (Triticum aestivum L.) TAXI-type endoxylanase inhibitor

S. Sansen, C. Verboven, C. De Ranter, K. Gebruers, K. Brijs, C. M. Courtin, J. A. Delcour and A. Rabijns

Synopsis: Crystals of an endoxylanase inhibitor from Triticum aestivum L. have been prepared and proved to be suitable for successful structural analysis.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 747-748  [ doi:10.1107/S0907444903003044 ]

Purification, characterization and preliminary X-ray crystallographic studies on Neiserria gonorrhoeae Gly1ORF1

D. N. Arvidson, R. F. Pearson and C. G. Arvidson

Synopsis: Recombinant Gly1ORF1 has been expressed, purified and crystallized. SeMet-substituted crystals were also prepared, aiming towards the three-dimensional structure solution via MAD methods.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 749-751  [ doi:10.1107/S0907444903003299 ]

Crystallization and X-ray diffraction analysis of the sensor domain of the HemAT aerotactic receptor

W. Zhang and G. N. Phillips

Synopsis: HemAT protein is responsible for sensing oxygen for Bacillus subtilis. The sensor domain of HemAT was cloned, expressed, crystallized and its structure is determined by a MAD method.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 752-754  [ doi:10.1107/S0907444903003408 ]

Crystallization, preliminary X-ray analysis and molecular-replacement solution of haemoglobin-II from the fish matrinxã (Brycon cephalus)

J. C. L. Fonseca, R. T. Honda, P. Delatorre, V. Fadel, G. O. Bonilla-Rodriguez and W. F. de Azevedo

Synopsis: The crystallization and preliminary X-ray analysis of the major haemoglobin (BcHb-II) from the fish matrinxã (B. cephalus) is reported.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 755-757  [ doi:10.1107/S0907444903003718 ]

Purification, crystallization and preliminary X-ray analysis of the Enterococcus faecalis protein EF0377

A. Riboldi-Tunnicliffe, C. J. Bent, N. W. Isaacs and T. J. Mitchell

Synopsis: The crystallization and preliminary X-ray diffraction of EF0377 is reported.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 758-760  [ doi:10.1107/S090744490300372X ]

Cloning, overexpression, purification, crystallization and preliminary diffraction analysis of the receiver domain of MicA

C. J. Bent, N. W. Isaacs, T. J. Mitchell and A. Riboldi-Tunnicliffe

Synopsis: The 14  kDa receiver domain of MicA response regulator from S. pneumoniae has been crystallized and its preliminary crystallographic data recorded.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 761-764  [ doi:10.1107/S0907444903002920 ]

Characterization and crystallization of active domains of a novel luciferase from a marine dinoflagellate

L. Liu, H. Im, M. Cegielski, P. LeMagueres, L. W. Schultz, K. L. Krause and J. W. Hastings

Synopsis: Two homologous domains from a dinoflagellate luciferase responsible for seawater bioluminescence have been prepared and crystallized. Domain D2 crystallized in space group P2₁2₁2₁ and diffracts to 2.8  Å on a rotating anode. Domain D3 crystals were grown in space group P2₁2₁2₁ and diffract to 2.3  Å on a rotating anode.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 765-768  [ doi:10.1107/S0907444903002051 ]

Structure of 20K endoglucanase from Melanocarpus albomyces at 1.8  Å resolution

J. Valjakka and J. Rouvinen

Synopsis: The three-dimensional structure of the uncomplexed 20K endoglucanase from the thermophilic fungus M. albomyces is mostly similar to that of previously determined family 45 endoglucanases, except that the flexible loop between strands V and VI is well ordered. Thermophilic and mesophilic endoglucanases of this family can now be compared.

PDB reference: 1l8f

Online 25 March 2003

 

Acta Cryst. (2003). D59, 769-772  [ doi:10.1107/S0907444903002919 ]

Comparison of three commercial sparse-matrix crystallization screens

J. W. Wooh, R. D. Kidd, J. L. Martin and B. Kobe

Synopsis: The efficiency of three commercially available crystallization screens was compared using 19 different proteins. The study identifies the most successful crystallization conditions in these screens and some general trends in the effectiveness of individual crystallization components.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 773-776  [ doi:10.1107/S0907444903002178 ]

Crystallization of the collagen-like polypeptide (PPG)₁₀ aboard the International Space Station. 3. Analysis of residual acceleration-induced motion

D. Castagnolo, C. Piccolo, L. Carotenuto, A. Vergara and A. Zagari

Synopsis: Acceleration data registered onboard the ISS have been analysed in combination with observed (PPG)₁₀ crystal motions and crystal quality.

Online 25 March 2003

 

Acta Cryst. (2003). D59, 777-782  [ doi:10.1107/S0907444903000805 ]

Inter-union bioinformatics group report

Online 25 March 2003