Biological Crystallography

 

Acta Cryst. (2004). D60, 621-629  [ doi:10.1107/S0907444904000915 ]

Diffraction and imaging study of imperfections of crystallized lysozyme with coherent X-rays

Z. W. Hu, Y. S. Chu, B. Lai, B. R. Thomas and A. A. Chernov

Synopsis: Individual line defects, inclusions and other microdefects were observed in the phase-contrast X-ray diffraction images of a tetragonal lysozyme crystal which had a 4 4 0 rocking-curve width of 16.7 arcsec. It was revealed that dehydration led to a significant change in the microstructures and a nearly threefold increase in the width of the 4 4 0 rocking curve.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 630-637  [ doi:10.1107/S0907444904001805 ]

Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium binding

K. Harata and T. Akiba

Synopsis: The phase transition of a triclinic lysozyme crystal was measured by X-ray diffraction and the structure of the transformed crystal was determined at 1.1 Å resolution.

PDB references: 1v7s and 1v7t

Online 23 March 2004

 

Acta Cryst. (2004). D60, 638-645  [ doi:10.1107/S0907444904002148 ]

Metals in the sporulation phosphorelay: manganese binding by the response regulator Spo0F

D. Mukhopadhyay, U. Sen, J. Zapf and K. I. Varughese

Synopsis: This paper reports the crystal structure of the response regulator Spo0F in complex with manganese and explores the differing possibilities for the involvement of manganese and magnesium in the phosphoryl transfer.

PDB reference: 1pey

Online 23 March 2004

 

Acta Cryst. (2004). D60, 646-655  [ doi:10.1107/S0907444904002094 ]

Structure determination of tetrahydroquinazoline antifolates in complex with human and Pneumocystis carinii dihydrofolate reductase: correlations between enzyme selectivity and stereochemistry

V. Cody, J. R. Luft, W. Pangborn, A. Gangjee and S. F. Queener

Synopsis: Structural data are reported for the first examples of the tetrahydroquinazoline antifolate (6R,6S)-2,4-diamino-6-(1-indolinomethyl)-5,6,7,8-tetrahydroquinazoline and its trimethoxy analogue (6R,6S)-2,4-diamino-6-(3',4',5'-trimethoxybenzyl)-5,6,7,8-tetrahydroquinazoline as inhibitor complexes with dihydrofolate reductase (DHFR) from human (hDHFR) and Pneumocystis carinii (pcDHFR) sources.

PDB references: 1s3w, 1s3y, 1s3u and 1s3v

Online 23 March 2004

 

Acta Cryst. (2004). D60, 656-664  [ doi:10.1107/S0907444904002239 ]

Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the T-cell ligand T10

M. G. Rudolph, C. Wingren, M. P. Crowley, Y. Chien and I. A. Wilson

Synopsis: The crystal structure of the T-cell ligand T10 was determined by molecular replacement using data from highly pseudo-merohedrally twinned monoclinic crystals that display pseudo-translation and non-crystallographic symmetry. The detection and treatment of twinning in T10 crystals and an analysis of the effect of the twinning on refinement is presented. A search of the PDB revealed several cases where possible twinning in monoclinic crystals may have gone unnoticed.

PDB reference: 1r3h

Online 23 March 2004

 

Acta Cryst. (2004). D60, 665-673  [ doi:10.1107/S090744490400232X ]

Structures of two lectins from the roots of pokeweed (Phytolacca americana)

T. Fujii, M. Hayashida, M. Hamasu, M. Ishiguro and Y. Hata

Synopsis: The crystal structures of two lectins from the roots of pokeweed (P. americana) have been solved by molecular replacement. Structural features are observed in the relative arrangement of the carbohydrate-binding sites and the C-terminal regions.

PDB references: 1uln and 1uha

Online 23 March 2004

 

Acta Cryst. (2004). D60, 674-679  [ doi:10.1107/S0907444904002549 ]

Structure of human translin at 2.2 Å resolution

I. Sugiura, C. Sasaki, T. Hasegawa, T. Kohno, S. Sugio, H. Moriyama, M. Kasai and T. Matsuzaki

Synopsis: A new crystal form of translin, an octameric human DNA/RNA-binding protein, has been solved at 2.2 Å resolution.

PDB reference: 1j1j

Online 23 March 2004

 

Acta Cryst. (2004). D60, 680-685  [ doi:10.1107/S0907444904002896 ]

DNA variability in five crystal structures of d(CGCAATTGCG)

N. Valls, G. Wright, R. A. Steiner, G. N. Murshudov and J. A. Subirana

Synopsis: A new structure of the duplex d(CGCAATTGCG)₂ is presented. It contains Co²⁺ and diffracts to 1.6 Å. The results obtained are compared with four structures of the same duplex previously reported. The central hexamer sequence CAATTG has a practically constant conformation under all conditions, whereas the terminal base pairs differ in each case.

PDB reference: 1s23

NDB reference: BD0066

Online 23 March 2004

 

Acta Cryst. (2004). D60, 686-695  [ doi:10.1107/S0907444904003002 ]

Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing

M. S. Weiss, G. Mander, R. Hedderich, K. Diederichs, U. Ermler and E. Warkentin

Synopsis: The structure of the 115-amino-acid residue protein DsvC was determined by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.

PDB reference: 1sau

Online 23 March 2004

 

Acta Cryst. (2004). D60, 696-702  [ doi:10.1107/S0907444904003154 ]

Assessing crystallization droplets using birefringence

A. Echalier, R. L. Glazer, V. Fülöp and M. A. Geday

Synopsis: An automated birefringence technique for assessing the content of crystallization droplets, in particular precipitates, is described and discussed.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 703-705  [ doi:10.1107/S090744490400109X ]

Crystallization and X-ray analysis of bovine glycolipid transfer protein

G. West, Y. Nymalm, T. T. Airenne, H. Kidron, P. Mattjus and T. T. Salminen

Synopsis: Glycolipid-transfer protein (GLTP) is a 24 kDa basic cytosolic protein that facilitates the transfer of glycolipids between bilayer membranes in vitro, but its in vivo function is unknown. Here, the crystallization and preliminary X-ray analysis of bovine GLTP are reported for the first time.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 706-708  [ doi:10.1107/S0907444904001398 ]

Crystallization and preliminary X-ray analysis of the Plasmodium vivax sexual stage 25 kDa protein Pvs25, a transmission-blocking vaccine candidate for malaria

A. K. Saxena, A. Saul and D. N. Garboczi

Synopsis: The anti-malaria vaccine candidate Pvs25 forms crystals that diffract to 2.3 Å and several complete data sets have been collected. The reductive methylation of lysine residues markedly improved the diffraction quality of the crystals.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 709-711  [ doi:10.1107/S0907444904001519 ]

Purification, crystallization and preliminary X-ray analysis of uridine phosphorylase from Salmonella typhimurium

M. V. Dontsova, Y. A. Savochkina, A. G. Gabdoulkhakov, S. N. Baidakov, A. V. Lyashenko, M. Zolotukhina, L. Errais Lopes, M. B. Garber, E. Y. Morgunova, S. V. Nikonov, A. S. Mironov, S. E. Ealick and A. M. Mikhailov

Synopsis: Uridine phosphorylase from S. typhimurium has been crystallized. A preliminary X-ray diffraction data set indicates that the crystals belong to space group P6₁₍₅₎.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 712-714  [ doi:10.1107/S0907444904001647 ]

Purification, crystallization and preliminary X-ray diffraction analysis of human oncoprotein SET/TAF-1

S. Muto, M. Senda, N. Adachi, T. Suzuki, R. Nagai, T. Senda and M. Horikoshi

Synopsis: The human oncoprotein SET/TAF-1 has been crystallized by the sitting-drop method. A complete diffraction data set was collected to 2.8 Å resolution using synchrotron radiation.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 715-717  [ doi:10.1107/S0907444904001854 ]

Crystallization and preliminary X-ray diffraction analysis of the hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum

M. W. Bhuiya, H. Sakuraba, K. Yoneda, T. Ohshima, T. Imagawa, N. Katunuma and H. Tsuge

Synopsis: Hyperthermostable NAD-dependent glutamate dehydrogenase from Pb. islandicum has been crystallized. The crystals diffract to a maximum resolution of 2.8 Å.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 718-720  [ doi:10.1107/S0907444904001969 ]

Crystallization and preliminary X-ray study of the common edible mushroom (Agaricus bisporus) lectin

M. E. Carrizo, F. J. Irazoqui, R. D. Lardone, G. A. Nores, J. A. Curtino, S. Capaldi, M. Perduca and H. L. Monaco

Synopsis: The common edible mushroom (A. bisporus) lectin has been crystallized in a form suitable for X-ray diffraction studies. The crystals diffract to 2.2 Å resolution.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 721-724  [ doi:10.1107/S0907444904002008 ]

Gene design, expression, crystallization and preliminary diffraction analysis of two isolectins from the fungus Coprinus cinereus: a model for studying functional diversification of galectins in the same organism and their evolutionary pathways

M. F. López-Lucendo, G. Giménez-Gallego, D. N. W. Cooper, H.-J. Gabius and A. Romero

Synopsis: Galectins are lectins involved in cell adhesion and growth regulation in animal cells. Cgl-1 and Cgl-2 of the fungus C. cinereus are the first family members from outside the animal kingdom. The gene design, expression, purification and crystallization of these two prototype galectins are described.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 725-726  [ doi:10.1107/S0907444904001866 ]

Crystallization and preliminary X-ray analysis of HCE-1, a hatching enzyme of medaka fish, Oryzias latipes

N. Kudo, S. Yasumasu, I. Iuchi and M. Tanokura

Synopsis: The hatching enzyme of medaka fish, high choriolytic enzyme has been crystallized by the hanging-drop vapour-diffusion method using PEG 10 000 as the precipitant.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 727-729  [ doi:10.1107/S0907444904002112 ]

Crystallization and preliminary crystallographic analysis of the circadian clock protein KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1

R. Iwase, K. Imada, F. Hayashi, T. Uzumaki, K. Namba and M. Ishiura

Synopsis: KaiB and Cys-substituted KaiB mutants from the thermophilic cyanobacterium T. elongatus BP-1 have been expressed as GST-fusion proteins in Escherichia coli, purified and crystallized.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 730-732  [ doi:10.1107/S0907444904002136 ]

Crystallization of a Golgi-associated PR-1-related protein (GAPR-1) that localizes to lipid-enriched microdomains

M. R. Groves, A. Kuhn, A. Hendricks, S. Radke, R. L. Serrano, J. B. Helms and I. Sinning

Synopsis: A human homologue of plant pathogenesis-related protein, which is specifically localized to the Golgi membranes, has been crystallized and crystals that diffract to 1.5 Å resolution are reported.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 733-735  [ doi:10.1107/S0907444904002021 ]

Crystallization and preliminary X-ray analysis of a conserved hypothetical protein PAE2754 from Pyrobaculum aerophilum and of a double LeuMet mutant engineered for MAD phasing

K. Bäckbro, A. Roos, E. N. Baker and V. L. Arcus

Synopsis: A conserved hypothetical protein from the hyperthermophilic crenarchaeon P. aerophilum has been expressed, purified and crystallized. Two methionine residues have been introduced by mutagenesis in order to provide SeMet-substituted crystals for MAD phasing.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 736-739  [ doi:10.1107/S0907444904002252 ]

Purification and crystallization of Escherichia coli oligoribonuclease

T. J. Fiedler, H. A. Vincent, Y. Zuo, O. Gavrialov and A. Malhotra

Synopsis: Oligoribonuclease (Orn), an essential 3'-to-5' exoribonuclease which degrades small oligoribonucleotides, has been crystallized under three different conditions.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 740-742  [ doi:10.1107/S0907444904002318 ]

Preliminary crystallographic analysis of the complex of the human GTPase RhoA with the DH/PH tandem of PDZ-RhoGEF

A. Oleksy, H. Barton, Y. Devedjiev, M. Purdy, U. Derewenda, J. Otlewski and Z. S. Derewenda

Synopsis: The DH/PH tandem of PDZ-RhoGEF and C-terminally truncated RhoA have been overexpressed in Escherichia coli as TEV protease-cleavable fusion proteins containing GST and a hexahistidine tag at the N-termini, respectively. The nucleotide-free DH/PH-RhoA complex was purified by gel filtration and crystallized.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 743-745  [ doi:10.1107/S090744490400229X ]

Crystallization and preliminary crystallographic analysis of the NAD(H)-binding domain of Escherichia coli transhydrogenase

C. Oswald, T. Johansson, S. Törnroth, M. Ökvist and U. Krengel

Synopsis: The NAD(H)-binding domain of the membrane protein transhydrogenase from E. coli has been crystallized. Crystals diffract to 1.9 Å resolution.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 746-748  [ doi:10.1107/S0907444904002410 ]

Expression, purification, crystallization and preliminary crystallographic studies of the Enterococcus faecalis cytolysin repressor CylR2

A. Razeto, K. Giller, W. Haas, M. S. Gilmore, M. Zweckstetter and S. Becker

Synopsis: The E. faecalis cytolysin repressor CylR2 forms part of a new quorum-sensing system.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 749-751  [ doi:10.1107/S0907444904002367 ]

Crystallization and preliminary X-ray crystallographic investigations of an unusual type III polyketide synthase PKS18 from Mycobacterium tuberculosis

R. Rukmini, V. M. Shanmugam, P. Saxena, R. S. Gokhale and R. Sankaranarayanan

Synopsis: Type III polyketide synthase PKS18 from M. tuberculosis has been crystallized in order to understand its unusual starter molecule specificity.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 752-754  [ doi:10.1107/S0907444904002392 ]

Purification, crystallization and preliminary structural characterization of human Rap1GAP

O. Daumke, A. Wittinghofer and M. Weyand

Synopsis: Rap1GAP, the founding member of a family of GTPase-activating proteins for the small GTPase Rap1, has been overexpressed, purified and crystallized. Data collection from native crystals is reported.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 755-757  [ doi:10.1107/S0907444904002422 ]

Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis

R. Bienert, M. Zeeb, L. Dostál, A. Feske, C. Magg, K. Max, H. Welfle, J. Balbach and U. Heinemann

Synopsis: The major cold-shock proteins of Bacillus subtilis and Bacillus caldolyticus are small oligonucleotide/oligosaccharide-binding fold proteins that have been described as binding single-stranded nucleic acids. Here they have been crystallized in the presence of the deoxyhexanucleotide (dT)₆.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 758-760  [ doi:10.1107/S0907444904002574 ]

Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli

K. E. van Straaten, B. W. Dijkstra and A.-M.W.H. Thunnissen

Synopsis: The crystallization and preliminary X-ray analysis of a soluble form of the lytic transglycosylase MltA that lacks the membrane anchor is presented.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 761-763  [ doi:10.1107/S0907444904002665 ]

Crystallization and preliminary crystallographic analysis of 2-keto-3-deoxygluconate kinase from Thermus thermophilus

E. Inagaki, Y. Ukita, M. Kumei, Y. Kajihara and T. H. Tahirov

Synopsis: Two crystal forms of 2-keto-3-deoxygluconate kinase from T. thermophilus have been obtained and characterized by X-ray diffraction.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 764-766  [ doi:10.1107/S0907444904003014 ]

Crystallization and preliminary X-ray analysis of two inhibitor complexes of the catalytic domain of death-associated protein kinase

A. Yamakawa, H. Ogata, K. Morita, N. Shibata, N. Andou, H. Sanuki, K. Yamada, T. Hioki, T. Ishii and Y. Higuchi

Synopsis: Single crystals of the catalytic domain of death-associated protein kinase and its complexes with two inhibitor molecules have been prepared using the sitting-drop vapour-diffusion method. Both inhibitor molecules were clearly identified in the resulting difference Fourier map.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 767-769  [ doi:10.1107/S0907444904003117 ]

Crystallization and preliminary X-ray diffraction data of an archaeal asparagine synthetase related to asparaginyl-tRNA synthetase

C. Charron, H. Roy, M. Blaise, R. Giegé and D. Kern

Synopsis: Crystals of asparagine synthetase A from the archaea P. abyssi, an enzyme structurally related to asparaginyl-tRNA synthetase, were grown by vapour diffusion; they belong to space groups C2 and P2₁ and diffract to 2.3 and 3.0 Å, respectively.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 770-772  [ doi:10.1107/S0907444904003221 ]

Crystallization and X-ray analysis of the Y75N mutant of Mucor pusillus pepsin complexed with inhibitor

M. O. Badasso, V. Dhanaraj, S. P. Wood, J. B. Cooper and T. L. Blundell

Synopsis: Y75N mutant M. pusillus pepsin has been cocrystallized with human renin inhibitor and the crystals have been analysed.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 773-774  [ doi:10.1107/S0907444904003282 ]

Crystallization and preliminary X-ray analysis of the acyl carrier protein synthase (AcpS) from Staphylococcus aureus

D. L. Daubaras, E. M. Wilson, T. Black, C. Strickland, B. M. Beyer and P. Orth

Synopsis: Acyl carrier protein synthase from S. aureus was crystallized in two crystal forms. Complete data sets were collected to resolutions of 1.65 and 1.8 Å, respectively.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 775-776  [ doi:10.1107/S0907444904003506 ]

Expression, purification, crystallization and preliminary diffraction studies of the tRNA pseudouridine synthase TruD from Escherichia coli

U. B. Ericsson, M. E. Andersson, B. Engvall, P. Nordlund and B. M. Hallberg

Synopsis: The tRNA pseudouridine synthase TruD from E. coli has been overexpressed, purified and crystallized. The orthorhombic crystals diffract to 2.4 Å resolution using synchrotron radiation.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 777-779  [ doi:10.1107/S0907444904004366 ]

Expression, purification, crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis thioredoxin reductase

M. Akif, R. Chauhan and S. C. Mande

Synopsis: Recombinant M. tuberculosis thioredoxin reductase has been expressed, purified and crystallized. Diffraction data were collected to 3 Å resolution and preliminary X-ray diffraction analysis is described.

Online 23 March 2004

    

Acta Cryst. (2004). D60, 780-783  [ doi:10.1107/S0907444904001544 ]

Characterization, crystallization and preliminary X-ray analysis of bifunctional dihydrofolate reductase-thymidylate synthase from Plasmodium falciparum

P. Chitnumsub, J. Yavaniyama, J. Vanichtanankul, S. Kamchonwongpaisan, M. D. Walkinshaw and Y. Yuthavong

Synopsis: Wild-type and mutant (C59R+S108N) dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) enzymes from P. falciparum complexed with NADPH, dUMP and either Pyr39 or Pyr30, pyrimethamine derivatives which retain binding affinities to the mutant enzyme, have been crystallized using the microbatch method. A preliminary study on the use of baby oil in microbatch crystallization is also discussed.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 784-787  [ doi:10.1107/S0907444904002628 ]

Crystallization, microPIXE and preliminary crystallographic analysis of the complex between the third KH domain of hnRNP K and single-stranded DNA

P. H. Backe, R. B. G. Ravelli, E. Garman and S. Cusack

Synopsis: Co-crystallization of the third KH domain of human hnRNP K with a 15-mer ssDNA gave rod-shaped crystals belonging to the trigonal space group P3₁21 (unit-cell parameters a = 54.0, c = 149.7 Å) and diffracting to 2.4 Å resolution.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 788-791  [ doi:10.1107/S0907444904002963 ]

Purification, crystallization and X-ray diffraction analysis of a recombinant Fab that recognizes a human blood-group antigen

S.-C. Song, K. Xie, M. Czerwinski, S. L. Spitalnik and J. E. Wedekind

Synopsis: The purification, crystallization and X-ray diffraction analysis of NNA7, an anti-blood group Fab fragment, are described along with initial phasing information.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 792-795  [ doi:10.1107/S0907444904003166 ]

Structure of bovine carbonic anhydrase II at 1.95 Å resolution

R. Saito, T. Sato, A. Ikai and N. Tanaka

Synopsis: The crystal structure of bovine carbonic anhydrase II (BCA II) has been determined at 1.95 Å resolution by molecular replacement.

PDB reference: 1v9e

Online 23 March 2004

 

Acta Cryst. (2004). D60, 796-799  [ doi:10.1107/S0907444904001982 ]

On the potential of normal-mode analysis for solving difficult molecular-replacement problems

K. Suhre and Y.-H. Sanejouand

Synopsis: Perturbing protein structural models in the direction of their lowest-frequency normal modes can make them favourable templates for difficult molecular-replacement problems.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 800  [ doi:10.1107/S0907444904004998 ]

Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum. Addendum

M. Maher, M. Cross, M. C. J. Wilce, J. M. Guss and A. G. Wedd

Synopsis: An addendum to the paper by Maher et al. (2004), Acta Cryst. D60, 298-303.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 801  [ doi:10.1107/S0907444904005001 ]

Microseed matrix screening to improve crystals of yeast cytosine deaminase. Erratum

G. C. Ireton and B. L. Stoddard

Synopsis: An erratum to the paper by Ireton & Stoddard (2004), Acta Cryst. D60, 601-605.

Online 23 March 2004

 

Acta Cryst. (2004). D60, 802  [ doi:10.1107/S0907444904005104 ]

Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G·A pairs to form a functional G·A×A·G crossing. Erratum

T. Sunami, J. Kondo, I. Hirao, K. Watanabe, K. Miura and A. Takénaka

Synopsis: An erratum to the paper by Sunami et al. (2004), Acta Cryst. D60, 422-431.

Online 23 March 2004