Biological Crystallography

 

Acta Cryst. (2001). D57, 181-186  [ doi:10.1107/S0907444900018023 ]

WWWWhy does nature stutter? A survey of strands of repeated amino acids

E. F. Meyer and W. J. Tollett

Synopsis: A survey of available databases with highly improbable strings of single amino acids is tabulated. The paper concludes with a challenge to the crystallographic community to probe the structural origins of the structure-function relationship in this neglected area.

Online February 2001

 

Acta Cryst. (2001). D57, 187-193  [ doi:10.1107/S0907444900015614 ]

The three-dimensional structure of cytosolic bovine retinal creatine kinase

D. Tisi, B. Bax and A. Loew

Synopsis: Creatine kinase catalyses the reversible transfer of the phosphate moiety from phosphocreatine to ADP, generating creatine and ATP. The structure of a cytosolic brain-type creatine kinase at 2.3  Å is reported.

PDB reference: 1g0w

Online February 2001

 

Acta Cryst. (2001). D57, 194-200  [ doi:10.1107/S0907444900015766 ]

Structure of hydroxynitrile lyase from Manihot esculenta in complex with substrates acetone and chloroacetone: implications for the mechanism of cyanogenesis

H. Lauble, S. Förster, B. Miehlich, H. Wajant and F. Effenberger

Synopsis: The X-ray structure of hydroxynitrile lyase from M. esculenta has been studied in complexes with acetone and chloroacetone. The binding observed reveals that the enzyme utilizes a general base mechanism to catalyse the reaction. In conjunction with additional kinetic data, the substrate specificity is discussed.

PDB references: 1dwo and 1dwq

Online February 2001

 

Acta Cryst. (2001). D57, 201-212  [ doi:10.1107/S0907444900016814 ]

Exploration of the GM1 receptor-binding site of heat-labile enterotoxin and cholera toxin by phenyl-ring-containing galactose derivatives

E. Fan, E. A. Merritt, Z. Zhang, J. C. Pickens, C. Roach, M. Ahn and W. G. J. Hol

Synopsis: Heat-labile enterotoxin from E. coli (LT) and the closely related cholera toxin are responsible for a large number of severe diarrheal cases in patients worldwide. The crystallographic studies presented here show how compounds built from a galactose anchor and containing a variety of substituted phenyl-ring systems interact with the receptor-binding site of LT.

PDB references: 1efi, 1eei, 1fd7 and 1eef

Online February 2001

 

Acta Cryst. (2001). D57, 213-218  [ doi:10.1107/S0907444900017595 ]

Direct-methods determination of an RNA/DNA hybrid decamer at 1.15  Å resolution

G. W. Han

Synopsis: This paper presents the crystal structure determination of the RNA/DNA hybrid decamer, caaagaaaag/CTTTTCTTTG, from the polypurine tract of HIV-1 at 1.15  Å. This hybrid decamer is the largest macromolecular structure to date solved by ab initio direct methods at this lower limit of resolution.

PDB reference: 1g4q

NDB reference: ah0012

Online February 2001

 

Acta Cryst. (2001). D57, 219-224  [ doi:10.1107/S0907444900017042 ]

Structure of an RNA duplex with an unusual G·C pair in wobble-like conformation at 1.6  Å resolution

M. Perbandt, M. Vallazza, C. Lippmann, C. Betzel and V. A. Erdmann

Synopsis: The structure of the RNA duplex r(CUGGGCGG)·r(CCGCCUGG) has been determined at 1.6  Å resolution and refined to a final R factor of 18.3% (R_free = 24.1%).

NDB reference: ar0012

Online February 2001

 

Acta Cryst. (2001). D57, 225-232  [ doi:10.1107/S0907444900017388 ]

Design, X-ray crystallography, molecular modelling and thermal stability studies of mutant enzymes at site 172 of 3-isopropylmalate dehydrogenase from Thermus thermophilus

C. Qu, S. Akanuma, N. Tanaka, H. Moriyama and T. Oshima

Synopsis: The relationship between the thermostability of T. thermophilus IPMDH mutated at residue 172 and the hydrophobicity of the substituted residue is dependent on its detailed structure in the vicinity of the replaced residue.

PDB references: 1gc8, 1gc9 and 1g2u

Online February 2001

 

Acta Cryst. (2001). D57, 233-238  [ doi:10.1107/S0907444900014670 ]

MAD phasing with krypton

A. Cohen, P. Ellis, N. Kresge and S. M. Soltis

Synopsis: Phasing of two proteins, the 17  kDa Fe protein myoglobin from sperm whale (P. catodon) and an 18  kDa protein (SP18) from green abalone (H. fulgens), using Kr-edge MAD with frozen crystals demonstrates the feasibility of this technique as a routine method for structure determination.

Online February 2001

 

Acta Cryst. (2001). D57, 239-249  [ doi:10.1107/S0907444900015249 ]

Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics

Z. Dauter, M. Li and A. Wlodawer

Synopsis: The use of short cryosoaks with salts of halides such as Br^- for phasing macromolecular structures is discussed on the basis of successful experience with solving the structure of Pseudomonas carboxyl proteinase, an enzyme with molecular mass 40  kDa, by single-wavelength anomalous diffraction.

PDB reference: 1ga1

Online February 2001

 

Acta Cryst. (2001). D57, 250-253  [ doi:10.1107/S0907444900018606 ]

Direct-method-aided phasing of MAD data

Y. X. Gu, Y. D. Liu, Q. Hao, S. E. Ealick and H. F. Fan

Synopsis: MAD phases can be complemented and improved by incorporating a direct-method procedure.

Online February 2001

 

Acta Cryst. (2001). D57, 254-259  [ doi:10.1107/S0907444900015225 ]

Dynamic light-scattering analysis of full-length human RPA14/32 dimer: purification, crystallization and self-association

J. E. Habel, J. F. Ohren and G. E. O. Borgstahl

Synopsis: The use of dynamic light scattering to improve purification, improve crystallization and to study the self-association of full-length human replication protein A heterodimer is described.

Online February 2001

 

Acta Cryst. (2001). D57, 260-262  [ doi:10.1107/S0907444900016851 ]

Crystallization of full-length CysB of Klebsiella aerogenes, a LysR-type transcriptional regulator

K. H. G. Verschueren, C. Addy, E. J. Dodson and A. J. Wilkinson

Synopsis: Crystals of intact tetrameric CysB from K. aerogenes have been obtained with and without its inducer N-acetylserine and in four different crystal forms.

Online February 2001

 

Acta Cryst. (2001). D57, 263-265  [ doi:10.1107/S090744490001516X ]

Crystallization and preliminary crystallographic studies of an antimicrobial protein from Pharbitis  nil

S. C. Ha, K. Min, J. C. Koo, Y. Kim, D. J. Yun, M. J. Cho and K. K. Kim

Synopsis: Antimicrobial protein from P. nil has been crystallized and native data have been collected at 1.78  Å resolution using synchrotron X-rays.

Online February 2001

 

Acta Cryst. (2001). D57, 266-268  [ doi:10.1107/S0907444900015237 ]

Crystallization and preliminary X-ray analysis of the 12S central subunit of transcarboxylase from Propionibacterium shermanii

Y.-F. Wang, D. C. Hyatt, R. E. Rivera, P. R. Carey and V. C. Yee

Synopsis: Several crystal forms of the 12S central subunit of the transcarboxylase multienzyme complex from P. shermanii have been grown. Co-crystallization with either methylmalonyl CoA or malonyl CoA substrate generates crystal forms with improved diffraction and co-crystallization with CdCl₂ further improves crystal stability.

Online February 2001

 

Acta Cryst. (2001). D57, 269-271  [ doi:10.1107/S0907444900015791 ]

Crystallization and preliminary studies of the DNA-binding runt domain of AML1

S. Bäckström, S.-H. Huang, M. Wolf-Watz, X.-Q. Xie, T. Härd, T. Grundström and U. H. Sauer

Synopsis: The DNA binding domain of AML1 has been crystallized in space groups C2 and R32 and it was found that adding DNA improved the crystal qualities, without incorporating DNA into the crystal lattice. Crystals diffract to 1.7 and 2.0  Å in C2 and R32, respectively.

Online February 2001

 

Acta Cryst. (2001). D57, 272-275  [ doi:10.1107/S0907444900016255 ]

Gene cloning, expression, crystallization and preliminary X-ray analysis of Thermus thermophilus arginyl-tRNA synthetase

A. Shimada, O. Nureki, N. Dohmae, K. Takio and S. Yokoyama

Synopsis: The gene for arginyl-tRNA synthetase from T. thermophilus was cloned and the recombinant protein was crystallized. X-ray data were collected from a flash-frozen native crystal to 2.3  Å resolution.

Online February 2001

 

Acta Cryst. (2001). D57, 276-278  [ doi:10.1107/S0907444900016243 ]

Crystallization and preliminary X-ray crystallographic analysis of the TM1442 gene product from Thermotoga maritima, a homologue of Bacillus subtilis anti-anti-sigma factors

K. S. Ha, J. E. Kwak, B. W. Han, J. Y. Lee, J. Moon, B. I. Lee and S. W. Suh

Synopsis: The TM1442 gene product from T. maritima has been overexpressed and crystallized (P2₁; a = 31.54, b = 116.83, c = 31.39  Å, = 119.84°). Diffraction data have been collected to 2.0  Å resolution using synchrotron X-rays.

Online February 2001

 

Acta Cryst. (2001). D57, 279-280  [ doi:10.1107/S0907444900016267 ]

Crystallization and preliminary X-ray crystallographic analysis of type II dehydroquinase from Helicobacter pylori

J. E. Kwak, J. Y. Lee, B. W. Han, J. Moon, S. H. Sohn and S. W. Suh

Synopsis: The type II dehydroquinase from H. pylori has been overexpressed and crystallized (P4₂32, a = b = c = 98.91  Å). Diffraction data have been collected to 2.5  Å resolution using synchrotron radiation.

Online February 2001

 

Acta Cryst. (2001). D57, 281-283  [ doi:10.1107/S0907444900016802 ]

Crystallization and preliminary X-ray diffraction analysis of the chloramphenicol acetyltransferase from Tn2424

M. Zhou, M.-L. Lu, W. Qiu, R. L. Campbell, V. Nahoum, J. Lapointe, P. H. Roy and S.-X. Lin

Synopsis: CAT B2 from Tn2424, a homotrimer of 3 × 23.5  kDa, has been crystallized; the space group of the crystal is P2₁3, with unit-cell parameter a = 130  Å. A complete data set has been collected at 2.7  Å resolution.

Online February 2001

 

Acta Cryst. (2001). D57, 284-286  [ doi:10.1107/S0907444900016838 ]

Crystallization and preliminary X-ray analysis of a -lactamase

I. S. Gonsalvez, M. N. Isupov and J. A. Littlechild

Synopsis: Crystals of -lactamase from C. acidovorans have been grown by the sitting-drop vapour-diffusion technique from recombinant protein expressed in E. coli. The triclinic crystals show diffraction to 2.0  Å resolution.

Online February 2001

 

Acta Cryst. (2001). D57, 287-288  [ doi:10.1107/S0907444900017571 ]

Preliminary structural studies of Escherichia coli isopentenyl diphosphate isomerase

Y. Oudjama, V. Durbecq, G. Sainz, B. Clantin, C. Tricot, V. Stalon, V. Villeret and L. Droogmans

Synopsis: E. coli isopentenyl diphosphate isomerase has been produced in selenomethionyl form and the protein was crystallized by the hanging-drop vapour-diffusion method. Crystals display trigonal symmetry with unit-cell parameters a = b = 71.3, c = 61.7  Å and diffract to 1.45  Å resolution.

Online February 2001

 

Acta Cryst. (2001). D57, 289-291  [ doi:10.1107/S0907444900017893 ]

Crystallization and preliminary X-ray diffraction analysis of the active core of human recombinant cystathionine -synthase: an enzyme involved in vascular disease

M. Janosik, M. Meier, V. Kery, J. Oliveriusova, P. Burkhard and J. P. Kraus

Synopsis: X-ray quality crystals have been obtained of a truncated form of cystathionine -synthase, an enzyme involved in vascular disease which contains both a PLP and a heme cofactor.

Online February 2001

 

Acta Cryst. (2001). D57, 292-295  [ doi:10.1107/S090744490001859X ]

Crystallization and preliminary X-ray analysis of the sporulation factor SpoIIAA in its native and phosphorylated forms

P. R. Seavers, R. J. Lewis, J. A. Brannigan and A. J. Wilkinson

Synopsis: Diffraction data to 1.6 and 2.25  Å resolution have been collected from crystals of the antisigma factor antagonist SpoIIAA from B. sphaericus in the native and phosphorylated forms, respectively.

Online February 2001

 

Acta Cryst. (2001). D57, 296-297  [ doi:10.1107/S0907444900019119 ]

Purification, crystallization and preliminary X-ray data for Escherichia coli GlmU: a bifunctional acetyltransferase/uridyltransferase

L. R. Olsen, Y. Tian and S. L. Roderick

Synopsis: Crystals of E. coli GlmU have been prepared in complex with coenzyme A and UDP-GlcNAc. These crystals belong to space group R32, with unit-cell parameters a = 104.5, c = 648.2  Å, and diffract X-rays to at least 2.1  Å resolution.

Online February 2001

 

Acta Cryst. (2001). D57, 298-300  [ doi:10.1107/S0907444900017546 ]

Crystallization and preliminary X-ray analysis of Borrelia burgdorferi outer surface protein C (OspC)

D. Kumaran, S. Eswaramoorthy, J. J. Dunn and S. Swaminathan

Synopsis: Outer surface protein C (OspC) from HB19 strain of B. burgdorferi has been crystallized and native data extending to 2.2  Å resolution have been collected.

Online February 2001

 

Acta Cryst. (2001). D57, 301-303  [ doi:10.1107/S0907444900017832 ]

Crystallization and preliminary X-ray diffraction analysis of a [2Fe-2S] ferredoxin (FdVI) from Rhodobacter capsulatus

J. Armengaud, G. Sainz, Y. Jouanneau and L. C. Sieker

Synopsis: A bacterial [2Fe-2S] ferredoxin possibly involved in iron-sulfur cluster biosynthesis has been crystallized for the first time. Crystals were obtained from the recombinant protein overproduced in E. coli; and a MAD experiment at the iron-edge is scheduled to solve the structure.

Online February 2001

 

Acta Cryst. (2001). D57, 304-305  [ doi:10.1107/S0907444900017030 ]

Crystallization and preliminary X-ray diffraction analysis of protein L-isoaspartyl O-methyltransferase from wheat germ

M. D. Amaral, L. Chen, D. Chattopadhyay, C. D. Smith and E. J. Meehan

Synopsis: WPIMT, a protein methyltransferase found in wheat germ, has been purified to homogeneity and crystallized in the presence of S-adenosine-L-homocysteine. The crystals diffract to 3.3  Å and belong to the tetragonal space group P4₁2₁2 or P4₃2₁2.

Online February 2001

 

Acta Cryst. (2001). D57, 306-309  [ doi:10.1107/S0907444900019429 ]

Identification of many crystal forms of Aspergillus nidulans dehydroquinate synthase

C. E. Nichols, J. Ren, H. Lamb, F. Haldane, A. R. Hawkins and D. K. Stammers

Synopsis: Nine different crystal forms of dehydroquinate synthase have been obtained and characterized. Crystals of complexes with inhibitor, cofactor as well as unliganded enzyme are described.

Online February 2001

 

Acta Cryst. (2001). D57, 310-313  [ doi:10.1107/S0907444900019727 ]

Crystallization and preliminary X-ray analysis of native and selenomethionine fructose-1,6-bisphosphate aldolase from Thermus aquaticus

V. Sauvé and J. Sygusch

Synopsis: Recombinant fructose-1,6-bisphosphate aldolase from the thermophile T. aquaticus was crystallized under two conditions. The native crystal grown under condition I diffracts to 2  Å and the SeMet crystal grown under condition II diffracts to 2.6  Å.

Online February 2001

 

Acta Cryst. (2001). D57, 314-316  [ doi:10.1107/S090744490001979X ]

Purification, crystallization and preliminary X-ray analysis of the Escherichia coli glucose-1-phosphatase

Z. Jia, M. Cottrill, G. P. Pal, D. Lee, M. Sung, C. W. Forsberg and J. P. Phillips

Synopsis: E. coli glucose-1-phosphatase hydrolyzes glucose-1-phosphate. The recombinant protein has been crystallized is space group R3, with two monomers in the asymmetric unit.

Online February 2001

 

Acta Cryst. (2001). D57, 317-319  [ doi:10.1107/S0907444900019739 ]

Crystallization and preliminary crystallographic study of the peptidoglycan-associated lipoprotein from Escherichia coli

C. Abergel, A. Walburger, S. Chenivesse and C. Lazdunski

Synopsis: Crystals of the 109 C-terminal residues of the E. coli Pal gene product have been produced. Selenomethionine-substituted truncated Pal protein is currently being produced in order to solve the Pal structure using the MAD method.

Online February 2001

 

Acta Cryst. (2001). D57, 320-322  [ doi:10.1107/S0907444900020825 ]

Crystallization and preliminary crystallographic study of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp)

C. Abergel, A. Abousalham, S. Chenivesse, M. Rivière, A.-M. Moustacas-Gardies and R. Verger

Synopsis: Crystals of the cowpea plant phospholipase D gene product have been produced. Crystals diffract to 1.94  Å. Heavy-atom derivatives using both the calcium binding site and the phospholipid binding site of the protein are currently being produced.

Online February 2001

 

Acta Cryst. (2001). D57, 323-325  [ doi:10.1107/S0907444900020837 ]

Crystallization and preliminary crystallographic study of the periplasmic domain of the Escherichia coli TolR protein

C. Abergel, L. Journet, S. Chenivesse, M. Gavioli and R. Lloubès

Synopsis: Crystals of the periplasmic domain of the E. coli TolR gene product have been produced. Selenomethionine-substituted truncated Pal protein is currently produced in order to solve the TolR structure using the MAD method.

Online February 2001

 

Acta Cryst. (2001). D57, 326-329  [ doi:10.1107/S0907444900015286 ]

Structure determination of bacterioferritin from Desulfovibrio desulfuricans by the MAD method at the Fe K-edge

A. V. Coelho, S. Macedo, P. M. Matias, A. W. Thompson, J. LeGall and M. A. Carrondo

Synopsis: Bacterioferritin isolated from D. desulfuricans was crystallized and its structure solved using MAD data collected at the K-shell iron edge.

Online February 2001

 

Acta Cryst. (2001). D57, 330-332  [ doi:10.1107/S0907444900017558 ]

An efficient method for solving RNA structures: MAD phasing by replacing magnesium with zinc

E. Ennifar, P. Walter and P. Dumas

Synopsis: The structure of a 46-nucleotide RNA complex has been successfully solved using multi-wavelength anomalous dispersion at the zinc K edge.

Online February 2001

 

Acta Cryst. (2001). D57, 333-336  [ doi:10.1107/S0907444900013779 ]

Structure of the laccase from Coprinus cinereus at 1.68  Å resolution: evidence for different `type 2 Cu-depleted' isoforms

V. Ducros, A. M. Brzozowski, K. S. Wilson, P. Østergaard, P. Schneider, A. Svendson and G. J. Davies

Synopsis: The three-dimensional structure of the `blue' multi-copper oxidase laccase from the fungus C. cinereus at 1.68  Å reveals the structural basis for isoforms of the type 2 Cu-depleted species.

PDB references: 1a65 and 1hfu

Online February 2001

 

Acta Cryst. (2001). D57, 337-340  [ doi:10.1107/S090744490001581X ]

Atomic resolution structure of a mutant of the spectrin SH3 domain

R. Berisio, A. Viguera, L. Serrano and M. Wilmanns

Synopsis: The crystal structure of an SH3 domain mutant has been refined at 1.12  Å resolution. This structure allows the interpretation on a molecular level of kinetic and thermodynamic experimental data.

PDB reference: 1g2b

Online February 2001

 

Acta Cryst. (2001). D57, 341-344  [ doi:10.1107/S090744490001800X ]

Structure of a new crystal form of tetraubiquitin

C. L. Phillips, J. Thrower, C. M. Pickart and C. P. Hill

Synopsis: Comparison of a new and previously determined structure of tetraubiuquitin reveals that the linkage between adjacent ubiquitin moieties is extremely flexible. This indicates that knowledge of relevant polyubiquitin conformations will require structures of polyubiquitin bound to target proteins.

PDB reference: 1f9j

Online February 2001

 

Acta Cryst. (2001). D57, 345-348  [ doi:10.1107/S0907444900017583 ]

Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?

M. Tsunoda, N. Karino, Y. Ueno, A. Matsuda and A. Takenaka

Synopsis: In crystallization of a Dickerson-type DNA dodecamer, a five-membered ring of water molecules can replace the hydrated magnesium cation to link neighboring duplexes in the crystal lattice, although the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution.

PDB references: 1g75, 1g8n, 1g8u and 1g8v

Online February 2001

 

Acta Cryst. (2001). D57, 349-354  [ doi:10.1107/S0907444900019934 ]

Protein crystallography with neutrons - status and perspectives

T. Gutberlet, U. Heinemann and M. Steiner

Synopsis: The current state of the art and future perspectives for protein crystallography with neutrons are reviewed and the relevance of neutrons in biology discussed briefly.

Online February 2001