Biological Crystallography

 

Acta Cryst. (2001). D57, 1755-1762  [ doi:10.1107/S0907444901013737 ]

Maximum-likelihood density modification using pattern recognition of structural motifs

T. C. Terwilliger

Synopsis: A likelihood-based density-modification method is extended to include pattern recognition of structural motifs.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1763-1775  [ doi:10.1107/S0907444901013749 ]

Map-likelihood phasing

T. C. Terwilliger

Synopsis: A map-likelihood function is described that can yield phase probabilities with very low model bias.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1776-1785  [ doi:10.1107/S0907444901014081 ]

Multiple isomorphous replacement on merohedral twins: structure determination of deacetoxycephalosporin C synthase

A. C. Terwisscha van Scheltinga, K. Valegård, S. Ramaswamy, J. Hajdu and I. Andersson

Synopsis: The structure of DAOCS was determined by isomorphous replacement from crystals twinned by merohedry.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1786-1792  [ doi:10.1107/S0907444901014482 ]

The first structure of pectate lyase belonging to polysaccharide lyase family 3

M. Akita, A. Suzuki, T. Kobayashi, S. Ito and T. Yamane

Synopsis: The structure of a low molecular-weight pectate lyase was determined at 1.5  Å resolution. The structure is a -helix domain motif.

PDB reference: 1ee6

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1793-1798  [ doi:10.1107/S0907444901014524 ]

Regulation of catalytic function by molecular association: structure of phospholipase A₂ from Daboia russelli pulchella (DPLA₂) at 1.9  Å resolution

V. Chandra, P. Kaur, J. Jasti, Ch. Betzel and T. P. Singh

Synopsis: The high-resolution X-ray analysis of phospholipase A₂ from D. russelli pulchella clearly brings out the differences between the two crystallographically independent molecules in the structure. The structure presents a unique case in which molecular association leads to blocking of the active site in one molecule while retaining the open geometry of the site in the other.

PDB reference: 1fb2

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1799-1812  [ doi:10.1107/S0907444901014949 ]

Spherical plant viruses: interactions in solution, phase diagrams and crystallization of brome mosaic virus

M. Casselyn, J. Perez, A. Tardieu, P. Vachette, J. Witz and H. Delacroix

Synopsis: Variations of interactions of brome mosaic viruses in solution and the immediate formation of microcrystals were characterized by small-angle X-ray scattering.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1813-1819  [ doi:10.1107/S0907444901015153 ]

Crystallographic analysis of family 11 endo--1,4-xylanase Xyl1 from Streptomyces sp. S38

J. Wouters, J. Georis, D. Engher, J. Vandenhaute, J. Dusart, J. M. Frere, E. Depiereux and P. Charlier

Synopsis: Family 11 endo--1,4-xylanases degrade xylan, the main constituent of plant hemicelluloses. The structure of a family 11 endo-xylanase from Streptomyces sp. S38 at 2.0  Å is reported.

PDB reference: 1hix

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1820-1828  [ doi:10.1107/S0907444901015414 ]

Conditional optimization: a new formalism for protein structure refinement

S. H. W. Scheres and P. Gros

Synopsis: An N-particle approach, combining loose-atom refinement with extensive application of geometrical restraints, allows optimization of a simple polyalanine test structure starting from random atom distributions.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1829-1835  [ doi:10.1107/S0907444901015475 ]

A twinned monoclinic crystal form of human peroxiredoxin 5 with eight molecules in the asymmetric unit

J.-P. Declercq and C. Evrard

Synopsis: The monoclinic crystal form of human peroxiredoxin 5 has been determined by the SIR method after detwinning. The presence of eight molecules in the asymmetric unit allows an analysis of the mobility.

PDB reference: 1h4o

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1836-1842  [ doi:10.1107/S0907444901015748 ]

Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study

R. B. Von Dreele

Synopsis: The binding of N-acetylglucosamine to chicken egg lysozyme was investigated by high-resolution X-ray powder diffraction.

PDB references: 1ja2, 1ja4, 1ja6 and 1ja7

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1843-1849  [ doi:10.1107/S0907444901016511 ]

Structure of Ca²⁺-loaded human grancalcin

J. Jia, N. Borregaard, K. Lollike and M. Cygler

Synopsis: The structure of full-length grancalcin, a cytosolic Ca²⁺-binding protein, has been determined in the apo form and with one EF-hand motif within the dimer occupied by a Ca²⁺ ion.

PDB references: 1k95 and 1k94

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1850-1856  [ doi:10.1107/S0907444901016493 ]

The structure of greylag goose oxy haemoglobin: the roles of four mutations compared with bar-headed goose haemoglobin

Y.-H. Liang, X.-Z. Liu, S.-H. Liu and G.-Y. Lu

Synopsis: The structure of the greylag goose oxy haemoglobin shows quaternary structural differences compared with that of its highland relative bar-headed goose. The four differing residues between the two species may be responsible for the differences in their oxygen affinity and quaternary structure.

PDB reference: 1faw

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1857-1862  [ doi:10.1107/S0907444901016535 ]

Matrix methods for solving protein substructures of chlorine and sulfur from anomalous data

R. A. G. de Graaff, M. Hilge, J. L. van der Plas and J. P. Abrahams

Synopsis: Using Karle-Hauptman matrices as the basis of an algebraic procedure of phase determination is proposed. The method allows the determination of the sulfur/chlorine substructure of lysozyme based on the anomalous signal obtained from in-house measurements.

Online 21 November 2001

    

Acta Cryst. (2001). D57, 1863-1869  [ doi:10.1107/S090744490101825X ]

The X-ray structure of a recombinant major urinary protein at 1.75  Å resolution. A comparative study of X-ray and NMR-derived structures

P. R. Kuser, L. Franzoni, E. Ferrari, A. Spisni and I. Polikarpov

Synopsis: The structure of a recombinant major urinary protein has been determined at 1.75  Å resolution. The crystal structure is compared with the NMR-derived structure.

PDB reference: 1jv4

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1870-1871  [ doi:10.1107/S0907444901014032 ]

Crystallization and preliminary X-ray diffraction analysis of shikimate kinase from Mycobacterium tuberculosis in complex with MgADP

Y. Gu, L. Reshetnikova, Y. Li, H. Yan, S. V. Singh and X. Ji

Synopsis: Shikimate kinase from M. tuberculosis has been overexpressed and purified to homogeneity. Crystals of the enzyme in complex with MgADP diffract to 2.2  Å resolution.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1872-1876  [ doi:10.1107/S0907444901014536 ]

Crystallization and preliminary X-ray diffraction analysis of two homologous antigen-binding fragments in complex with different carbohydrate antigens

H. P. Nguyen, N. O. L. Seto, L. Brade, P. Kosma, H. Brade and S. V. Evans

Synopsis: The crystallization of antigen-binding fragments from two homologous monoclonal antibodies in the presence and absence of different carbohydrate haptens offers an opportunity to determine the sequence-structural basis of carbohydrate specificity.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1877-1880  [ doi:10.1107/S0907444901014500 ]

Expression and preliminary X-ray diffraction studies of cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni

R. M. F. Cardoso, C. H. T. P. da Silva, A. P. U. de Araújo, T. Tanaka, M. Tanaka and R. C. Garratt

Synopsis: Cytosolic Cu,Zn superoxide dismutase from S. mansoni has been crystallized in both orthorhombic and monoclinic space groups and data have been collected to 2.2 and 1.55  Å, respectively. Molecular-replacement solutions show that slight distortions to the crystal lattice relate one form to the other.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1881-1884  [ doi:10.1107/S0907444901014937 ]

Crystallization and preliminary X-ray study of the edema factor exotoxin adenylyl cyclase domain from Bacillus anthracis in the presence of its activator, calmodulin

C. L. Drum, Y. Shen, P. A. Rice, A. Bohm and W.-J. Tang

Synopsis: A complex of human calmodulin and adenylyl cyclase domain of edema factor, a pathogenic factor secreted by Bacillus anthrax, was crystallized in space groups I222, P3₁21 and P2₁2₁2₁. The initial phases were obtained by selenomethionyl MAD using direct methods and improved by combining with two heavy-metal derivatives.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1885-1886  [ doi:10.1107/S0907444901015141 ]

Crystallization and preliminary X-ray analysis of W120K mutant of streptavidin

Y. Pazy, O. H. Laitinen, B. Ravoy, M. S. Kulomaa, M. Wilchek, E. A. Bayer and O. Livnah

Synopsis: Crystallization and data collection are reported of a streptavidin crucial tryptophan mutation (Savm-W120K) that results in decreased affinity towards biotin and the dissociation of the tetramer into stable dimers.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1887-1889  [ doi:10.1107/S0907444901015189 ]

Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Haloferax mediterranei

J. Ferrer, M. Fisher, J. Burke, S. E. Sedelnikova, P. J. Baker, D. J. Gilmour, M. J. Bonete, C. Pire, J. Esclapez and D. W. Rice

Synopsis: Recombinant glucose dehydrogenase from the halophilic archaea H. mediterranei has been refolded, purified and crystallized. Two crystal forms have been obtained, one of which diffracts to greater than 2.0  Å resolution.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1890-1892  [ doi:10.1107/S0907444901015360 ]

Crystallization and preliminary X-ray diffraction analysis of human transcobalamin, a vitamin B₁₂-transporting protein

G. Garau, S. N. Fedosov, T. E. Petersen, S. Geremia and L. Randaccio

Synopsis: Transcobalamin is a cobalamin-binding protein present in mammalian plasma that facilitates the cellular uptake of vitamin B₁₂. Crystals of human transcobalamin have been obtained and diffraction data have been collected to 3.2  Å resolution.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1893-1894  [ doi:10.1107/S0907444901015517 ]

Preliminary crystallographic studies of the double-stranded DNA-binding protein Sso10b from Sulfolobus solfataricus

B. N. Wardleworth, R. J. M. Russell, M. F. White and G. L. Taylor

Synopsis: Crystals of Sso10b, an abundant non-specific double-stranded DNA-binding protein, from the hyperthermophilic archaeon S. solfataricus have been grown and preliminary X-ray data are reported.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1895-1896  [ doi:10.1107/S0907444901015657 ]

Crystallization and preliminary crystallographic data of the PAS domain of the NifL protein from Azotobacter vinelandii

M. Hefti, J. Hendle, C. Enroth, J. Vervoort and P. A. Tucker

Synopsis: The PAS domain of the NifL protein from A. vinelandii has been crystallized and X-ray diffraction data have been collected to 3.0  Å using synchrotron radiation. The native crystals belong to space group R32, with unit-cell parameters a = 65.0, c = 157.3  Å.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1897-1899  [ doi:10.1107/S0907444901015815 ]

Crystallization and preliminary X-ray analysis of neural haemoglobin from the nemertean worm Cerebratulus lacteus

A. Pesce, M. Nardini, S. Dewilde, P. Ascenzi, A. F. Riggs, K. Yamauchi, E. Geuens, L. Moens and M. Bolognesi

Synopsis: A haemoglobin-related protein composed of 109 residues (i.e. 30% shorter than conventional vertebrate haemoglobins) has been isolated from a nemertean worm neural tissue. Crystals of the recombinant protein allow location of the haem Fe atom in anomalous difference Patterson maps.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1900-1902  [ doi:10.1107/S0907444901015852 ]

Crystallization and preliminary X-ray analysis of the periplasmic nitrate reductase (NapA-NapB complex) from Rhodobacter sphaeroides f. sp. denitrificans

D. Pignol, J.-M. Adriano, J.-C. Fontecilla-Camps and M. Sabaty

Synopsis: The heterodynamic periplasmic nitrate reductase from R. sphaeroides has been cloned, purified and crystallized. X-ray diffraction data have been collected to 3.1  Å resolution.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1903-1905  [ doi:10.1107/S0907444901016018 ]

Crystallization and preliminary X-ray study of two liver basic fatty acid-binding proteins

S. M. Di Pietro, M. Perduca, J. A. Santomé and H. L. Monaco

Synopsis: Two different liver basic fatty acid-binding proteins have been crystallized in forms suitable for X-ray diffraction studies. The crystals diffract to 2.0 and 2.5  Å resolution.

Online 21 November 2001

    

Acta Cryst. (2001). D57, 1906-1907  [ doi:10.1107/S0907444901016286 ]

Purification, crystallization and preliminary X-ray analysis of an acetylxylan esterase from Bacillus pumilus

S. Benini, G. Degrassi, I. Krastanova, D. Lamba and V. Venturi

Synopsis: Crystals of the acetylxylan esterase from B. pumilus have been obtained by the hanging-drop method. The crystals diffract to 2.0  Å resolution and belong to space group R32.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1908-1911  [ doi:10.1107/S0907444901016249 ]

Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1

K. Josephson, D. T. McPherson and M. R. Walter

Synopsis: Crystals of interleukin-10 in complex with the extracellular cytokine-binding domain of its high-affinity receptor have been obtained. A complete low-temperature native data set to 2.9  Å has been collected using synchrotron radiation.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1912-1914  [ doi:10.1107/S0907444901016274 ]

Crystallization and preliminary X-ray study of OXA-1, a class D -lactamase

T. Sun, M. Nukaga, K. Mayama, G. V. Crichlow, A. P. Kuzin and J. R. Knox

Synopsis: The OXA-1 oxacillinase from E. coli has been crystallized from PEG at pH 7.5 in P1. Crystals diffract to 1.5  Å resolution and contain two monomers related by a pseudo twofold screw axis.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1915-1918  [ doi:10.1107/S0907444901016298 ]

Crystallization and preliminary X-ray analysis of maltose O-acetyltransferase

L. Lo Leggio, F. Dal Degan, P. Poulsen, S. O. Sørensen, K. Harlow, P. Harris and S. Larsen

Synopsis: Maltose O-acetyltransferase has been crystallized in four crystal forms, including a trimethyl lead acetate cocrystal suitable for structure determination.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1919-1921  [ doi:10.1107/S0907444901016523 ]

Preparation and X-ray crystallographic analysis of recombinant obelin crystals diffracting to beyond 1.1  Å

E. S. Vysotski, Z.-J. Liu, J. Rose, B. C. Wang and J. Lee

Synopsis: Crystallization conditions are described that allow recombinant obelin from O. longissima to form relatively large single light yellow crystals with excellent diffraction properties. A 1.1  Å data set has been collected and analysis is in progress.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1922-1924  [ doi:10.1107/S0907444901016675 ]

Crystallization and preliminary X-ray analysis of Citrobacter amalonaticus methylaspartate ammonia lyase

C. W. Levy, P. A. Buckley, P. J. Baker, S. Sedelnikova, F. Rodgers, Y. F. Li, Y. Kato, Y. Asano and D. W. Rice

Synopsis: The purification and crystallization of C. amalonaticus (2S,3S)-3-methylaspartic acid ammonia lyase is reported. Diffraction data have been collected to 2.1 and 1.5  Å, respectively, from two different crystal forms.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1925-1927  [ doi:10.1107/S0907444901017140 ]

Crystallization and preliminary crystallographic analysis of the proline dehydrogenase domain of the multifunctional PutA flavoprotein from Escherichia coli

S. Nadaraia, Y.-H. Lee, D. F. Becker and J. J. Tanner

Synopsis: Crystals of a peptide corresponding to the first 669 residues of a 1320-residue multifunctional flavoprotein have been obtained and X-ray data have been collected to 2.15  Å resolution.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1928-1930  [ doi:10.1107/S090744490101722X ]

Crystallization and preliminary X-ray diffraction analysis of the 10  kDa C-terminal subdomain of 70  kDa heat-shock cognate protein

C.-C. Chou, C. Wang, Y.-J. Sun, H.-L. Shr and C.-D. Hsiao

Synopsis: The C-terminal subdomain of rat 70  kDa heat-shock cognate protein has been cloned and expressed in E. coli. Preliminary crystallographic investigations have been carried out.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1931-1932  [ doi:10.1107/S0907444901017280 ]

Crystallization and preliminary crystallographic studies of antibacterial polypeptide LCI expressed in Escherichia coli

J.-P. Zhu, B.-Z. Chen, W.-B. Gong, Y.-H. Liang, H.-C. Wang, Q. Xu, Z.-L. Chen and G.-Y. Lu

Synopsis: LCI, type of novel antibacterial polypeptide secreted by a Bacillus subtilis strain, has been expressed in E. coli DH5 with recombinant plasmid pBVAB16 and crystallized using PEG 4000 as a precipitant.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1933-1935  [ doi:10.1107/S0907444901017322 ]

Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 ClpB N-terminal domain

J. Li and B. Sha

Synopsis: The N-terminal domain of E. coli Hsp100 ClpB has been crystallized. The crystal diffracted X-rays to 1.95  Å.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1936-1937  [ doi:10.1107/S0907444901017334 ]

Crystallization and preliminary crystallographic analysis of human alanine:glyoxylate aminotransferase and its polymorphic variants

X. Zhang, S. M. Roe, L. H. Pearl and C. J. Danpure

Synopsis: Crystallization and preliminary crystallographic analysis has been carried out on the most common polymorphic variants of the human intermediary metabolic enzyme alanine:glyoxylate aminotransferase, a deficiency of which causes the autosomal recessive disease primary hyperoxaluria type 1.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1938-1944  [ doi:10.1107/S090744490101040X ]

Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine

D. J. Derbyshire, D. J. Ellar and J. Li

Synopsis: Aggregation of a membrane toxin was overcome by the use of the diamine buffer 1,3-diaminopropane. Glycerol inhibition of complex formation between protein and carbohydrate was shown to be insignificant in competitive binding assays conducted in the presence of glycerol prior to crystallization.

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1945-1949  [ doi:10.1107/S0907444901014512 ]

Crystallization and rhenium MAD phasing of the acyl-homoserinelactone synthase EsaI

W. T. Watson, F. V. Murphy, T. A. Gould, P. Jambeck, D. L. Val, J. E. Cronan, S. Beck von Bodman and M. E. A. Churchill

Synopsis: The acyl-homoserinelactone synthase EsaI has been crystallized in the space group P4₃, with unit-cell parameters a = b = 66.40, c = 47.33  Å. Multiple-wavelength anomalous diffraction using rhenium, a novel MAD atom, provided phases; the perrhenate-binding sites were identified in the model at 2.5  Å.

PDB reference: 1k4j

Online 21 November 2001

 

Acta Cryst. (2001). D57, 1950-1954  [ doi:10.1107/S090744490101575X ]

Structure of Haemophilus influenzae HslV protein at 1.9  Å resolution, revealing a cation-binding site near the catalytic site

M. C. Sousa and D. B. McKay

Synopsis: Anomalous scattering measurements reveal a K⁺ ion bound in proximity to the active site of the H. influenzae HslV protease.

PDB references: 1g3k and 1jjw

Online 21 November 2001