Biological Crystallography

 

Acta Cryst. (2004). D60, 211-219  [ doi:10.1107/S090744490302849X ]

Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure

S. Kundhavai Natchiar, A. Arockia Jeyaprakash, T. N. C. Ramya, C. J. Thomas, K. Suguna, A. Surolia and M. Vijayan

Synopsis: The rigid and the flexible regions of the peanut lectin molecule have been delineated and the invariant water molecules in its hydration shell identified using the structures of the lectin crystals containing ligand-bound and ligand-free subunits, grown under different environmental conditions. The molecule is sturdy and the combining site is essentially preformed.

PDB references: 1v6i, 1v6j, 1v6k, 1v6l, 1v6m, 1v6n and 1v6o

Online 24 January 2004

 

Acta Cryst. (2004). D60, 220-226  [ doi:10.1107/S0907444903025526 ]

The influence of positional errors on the Debye effects

P. H. Zwart and V. S. Lamzin

Synopsis: A relation between a Gaussian perturbation of the atomic positional parameters and the average squared structure-factor amplitude for the estimation of the quality of an atomic model and corresponding phases is presented.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 227-240  [ doi:10.1107/S0907444903025538 ]

On the interpretation and use of <|E|²>(d*) profiles

R. J. Morris, E. Blanc and G. Bricogne

Synopsis: A structural interpretation of <|E|²>(d*) curves is presented and their use for improved parameter estimation in scaling is discussed.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 241-249  [ doi:10.1107/S0907444903025873 ]

A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase

B. L. Hanson, P. Langan, A. K. Katz, X. Li, J. M. Harp, J. P. Glusker, B. P. Schoenborn and G. J. Bunick

Synopsis: Spallation neutron diffraction data have been measured to better than 2.0 Å resolution on the metalloenzyme D-xylose isomerase at the Protein Crystallography Station beamline at Los Alamos Neutron Science Center. This represents one of the largest proteins and unit cells (10⁶ Å³) to be studied to this resolution by neutron diffraction.

Online 24 January 2004

    

Acta Cryst. (2004). D60, 250-255  [ doi:10.1107/S0907444903025927 ]

Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu K diffraction data only

J. G. Olsen, C. Flensburg, O. Olsen, G. Bricogne and A. Henriksen

Synopsis: The previously unknown structure of a 64-residue fungal protein, denoted the bubble protein, was solved in a highly automated fashion using the anomalous scattering from eight S atoms in data collected on in-house equipment.

PDB reference: 1uoy

Online 24 January 2004

 

Acta Cryst. (2004). D60, 256-259  [ doi:10.1107/S090744490302599X ]

The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus

L. Prasad, Y. Leduc, K. Hayakawa and L. T. J. Delbaere

Synopsis: The crystal structure of the V8 protease from S. aureus is reported. From modeling studies, the residues of the enzyme involved in determining its unique specificity for acidic amino-acid residues are predicted.

PDB reference: 1qy6

Online 24 January 2004

 

Acta Cryst. (2004). D60, 260-274  [ doi:10.1107/S0907444903026209 ]

On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps

P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev

Synopsis: Conventional macromolecular refinement performed at a resolution near 0.6 Å allows regular bond-electron peaks to be observed in difference maps for individual bonds in well ordered molecular domains. These peaks are not visible in the maps if the refinement is performed at a resolution close to 0.9 Å.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 275-280  [ doi:10.1107/S0907444903026271 ]

The impact of LysArg surface mutations on the crystallization of the globular domain of RhoGDI

J. Czepas, Y. Devedjiev, D. Krowarsch, U. Derewenda, J. Otlewski and Z. S. Derewenda

Synopsis: As part of an ongoing effort, the usefulness of LysArg surface mutations in the globular domain of human RhoGDI is studied.

PDB reference: 1qvy

Online 24 January 2004

 

Acta Cryst. (2004). D60, 281-288  [ doi:10.1107/S0907444903026684 ]

Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction

M. Goel, P. Anuradha, K. J. Kaur, B. G. Maiya, M. J. Swamy and D. M. Salunke

Synopsis: The crystal structure of the meso-tetrasulphonatophenylporphyrin (H₂TPPS)-jacalin complex, determined at 1.8 Å resolution, exhibits binding of the pluripotent porphyrin molecule exploiting the plasticity of the carbohydrate binding site.

PDB reference: 1pxd

Online 24 January 2004

 

Acta Cryst. (2004). D60, 289-297  [ doi:10.1107/S0907444903027367 ]

Structure of the core region of the soybean -conglycinin ' subunit

Y. Maruyama, N. Maruyama, B. Mikami and S. Utsumi

Synopsis: The crystal structure of the core region of the soybean -conglycinin ' subunit has been determined at 2.3 Å resolution. The structural factors accounting for the difference in thermal stability between the subunits of -conglycinin are discussed.

PDB reference: 1uik

Online 24 January 2004

    

Acta Cryst. (2004). D60, 298-303  [ doi:10.1107/S090744490302794X ]

Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum

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

Synopsis: The single Fe atom in the Fe(S-Cys)₄ site of C. pasteurianum rubredoxin was exchanged in turn for Cd, Hg, Co, Ni and Ga and the structures of these derivatives were refined.

PDB references: 1r0f, 1r0g, 1r0h, 1r0i and 1r0j

Online 24 January 2004

 

Acta Cryst. (2004). D60, 304-309  [ doi:10.1107/S0907444903028695 ]

Structure of circularly permuted DsbA_Q100T99: preserved global fold and local structural adjustments

B. A. Manjasetty, J. Hennecke, R. Glockshuber and U. Heinemann

Synopsis: The X-ray structure of a circularly permuted variant of thiol-disulfide oxidoreductase, cpDsbA_Q100T99, is reported in which the natural termini are joined by the pentapeptide linker GGGTG, leading to a continuous thioredoxin domain, and new termini that have been introduced in the helical domain by breaking the peptide bond Thr99-Gln100.

PDB reference: 1un2

Online 24 January 2004

 

Acta Cryst. (2004). D60, 310-313  [ doi:10.1107/S090744490302910X ]

Crystallization and preliminary crystallographic data of a leucotoxin S component from Staphylococcus aureus

V. Guillet, D. Keller, G. Prévost and L. Mourey

Synopsis: The S component of the Panton-Valentine leucocidin from S. aureus has been crystallized. A complete native data set to 2.1 Å resolution has been collected.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 314-316  [ doi:10.1107/S0907444903028518 ]

Purification, crystallization and preliminary X-ray diffraction of a proteolytic fragment of PDK1 containing the pleckstrin homology domain

D. Komander, M. Deak, N. Morrice and D. M. F. van Aalten

Synopsis: The construct design by limited proteolysis, subsequent cloning, purification and crystallization of the PH domain of human PDK1 is reported, along with a Patterson map of a gold-derivatized crystal.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 317-319  [ doi:10.1107/S0907444903025770 ]

Crystallization and preliminary crystallographic analysis of rat monoamine oxidase A complexed with clorgyline

J. Ma, F. Kubota, M. Yoshimura, E. Yamashita, A. Nakagawa, A. Ito and T. Tsukihara

Synopsis: The crystallization of rat monoamine oxidase A and general considerations for the crystallization of membrane proteins are presented.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 320-322  [ doi:10.1107/S0907444903025897 ]

Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue

T. Sengoku, O. Nureki, N. Dohmae, A. Nakamura and S. Yokoyama

Synopsis: The helicase fragment of Vasa was crystallized in complex with poly(U) RNA and a non-hydrolyzable analogue of ATP. The crystal diffracted to 2.2 Å resolution.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 323-325  [ doi:10.1107/S0907444903026143 ]

Crystallization and preliminary X-ray analysis of the controller protein C.AhdI from Aeromonas hydrophilia

J. E. McGeehan, S. Streeter, J. B. Cooper, F. Mohammed, G. C. Fox and G. G. Kneale

Synopsis: Preliminary crystallographic analysis of the gene-regulatory protein C.AhdI from the bacterial restriction-modification system A. hydrophilia has been undertaken. Native and selenomethionine-derivative data were collected to resolutions of 2.2 and 1.7 Å, respectively.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 326-328  [ doi:10.1107/S0907444903026192 ]

Expression, purification and crystallization of an extended-spectrum -lactamase from Klebsiella oxytoca

S. W. Wu, Y.-H. Liang and X.-D. Su

Synopsis: An extended-spectrum -lactamase, OXY-1a, from K. oxytoca has been crystallized in two crystal forms which diffracted to different resolutions. The orthorhombic crystal diffracted to at least 1.9 Å and is thus suitable for high-resolution structural studies.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 329-330  [ doi:10.1107/S090744490302626X ]

Crystallization of YloQ, a GTPase of unknown function essential for Bacillus subtilis viability

L. Cladière, E. Blagova, V. M. Levdikov, J. A. Brannigan, S. J. Séror and A. J. Wilkinson

Synopsis: YloQ, a putative GTPase essential for the viability of B. subtilis, has been purified and crystallized. A complete diffraction data set to 2.5 Å spacing has been collected using synchrotron radiation.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 331-333  [ doi:10.1107/S0907444903026519 ]

Crystallization and preliminary X-ray diffraction analysis of a dihaem cytochrome c peroxidase from Paracoccus denitrificans

A. Echalier, C. F. Goodhew, G. W. Pettigrew and V. Fülöp

Synopsis: Two different crystal forms have been obtained of the fully oxidized form of the dihaem cytochrome c peroxidase from P. denitrificans. One of them diffracts X-rays beyond 2.3 Å resolution and is suitable for structure determination.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 334-336  [ doi:10.1107/S0907444903026696 ]

Expression, crystallization and preliminary X-ray studies of the recombinant PTB domain of mouse dok1 protein

N. Shi, Y. Liu, M. Ni, M. Yang, J. Wu, Y. Peng, F. Gao, F. Sun, X. Peng, B. Qiang, Z. Rao and J. Yuan

Synopsis: The PTB domain of mouse dok1 has been purified and crystallized. A selenomethionmine-substituted protein that diffracts to 2.5 Å resolution has been used to collect a full three-wavelength MAD data set.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 337-339  [ doi:10.1107/S0907444903026799 ]

Crystallization and preliminary X-ray diffraction analysis of an oxidized state of Ohr from Xylella fastidiosa

M. A. de Oliveira, L. E. S. Netto, F. J. Medrano, J. A. R. G. Barbosa, S. V. Alves, J. R. R. Cussiol and B. G. Guimarães

Synopsis: Recombinant Ohr was expressed in E. coli as a His₆-tagged fusion protein, purified by nickel-affinity chromatography and crystallized using PEG 4000 as precipitant after treatment with t-butyl hydroperoxide. Crystals belong to space group P6₅22, with unit-cell parameters a = b = 87.66, c = 160.28 Å, and diffract X-rays to a resolution of 1.8 Å.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 340-341  [ doi:10.1107/S0907444903027100 ]

Crystallization and preliminary crystallographic analysis of a novel orange fluorescent protein from the Cnidaria tube anemone Cerianthus sp.

D. T. M. Ip, S.-H. Chan, M. D. Allen, M. Bycroft, D. C. C. Wan and K.-B. Wong

Synopsis: A novel orange fluorescent protein from the Cnidaria tube anemone Cerianthus sp. was crystallized in space group R3, with hexagonal unit-cell parameters a = b = 216.947, c = 51.839 Å. A set of complete diffraction data was collected to 2.0 Å.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 342-343  [ doi:10.1107/S090744490302715X ]

Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium

M. Nishimoto, S. Fushinobu, A. Miyanaga, T. Wakagi, H. Shoun, K. Sakka, K. Ohmiya, S. Nirasawa, M. Kitaoka and K. Hayashi

Synopsis: A crystal of mature xylanase B from C. stercorarium has been prepared and the X-ray diffraction data have been collected to 1.80 Å resolution.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 344-346  [ doi:10.1107/S0907444903027227 ]

Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ

K. Brzezinski, B. Rogozinski, T. Stepkowski, G. Bujacz and M. Jaskolski

Synopsis: Native crystals of recombinant fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus) diffract X-rays to 2.85 Å resolution at 100 K. The crystals are hexagonal, space group P6₁22 or P6₅22, with unit-cell parameters a = 125.5, c = 95.6 Å, and contain one protein molecule in the asymmetric unit.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 347-349  [ doi:10.1107/S0907444903027240 ]

Crystallization and preliminary X-ray analysis of the human-specific toxin intermedilysin

G. Polekhina, K. S. Giddings, R. K. Tweten and M. W. Parker

Synopsis: Crystals of the human-specific toxin intermedilysin from S. intermedius have been obtained by manipulating the dialysis conditions prior to crystallization.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 350-352  [ doi:10.1107/S0907444903027628 ]

Expression, purification and crystallization of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1

S. Harjes, A. Scheidig and P. Bayer

Synopsis: Recombinant purified full-length human PAPS synthetase 1 migrates as a dimer in solution. Monoclinic crystal diffraction intensities have been measured to 1.75 Å resolution using synchrotron radiation.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 353-356  [ doi:10.1107/S090744490302763X ]

Crystallization and preliminary crystallographic analysis of Mycoplasma arthritidis-derived mitogen complexed with peptide/MHC class II antigen

Y. Zhao, Z. Li, S. Drozd, Y. Guo, R. Stack, C. Hauer and H. Li

Synopsis: The crystallization and preliminary crystallographic analysis of M. arthritidis-derived mitogen complexed with peptide/MHC class II antigen is described.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 357-358  [ doi:10.1107/S0907444903027458 ]

Expression, purification, crystallization and preliminary crystallographic analysis of osmotically inducible protein C

P. H. Rehse, Y. Nodake, C. Kuroishi and T. H. Tahirov

Synopsis: The osmotically inducible protein C from T. thermophilus was overexpressed, purified and crystallized. Data were collected at five wavelengths for MAD phasing and the unit-cell contents were analyzed.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 359-361  [ doi:10.1107/S0907444903027720 ]

Expression, purification, crystallization and preliminary characterization of uridine 5'-diphospho-N-acetylmuramoyl L-alanyl-D-glutamate:lysine ligase (MurE) from Streptococcus pneumoniae 110K/70

A. M. Blewett, A. J. Lloyd, A. Echalier, V. Fülöp, C. G. Dowson, T. D. H. Bugg and D. I. Roper

Synopsis: An open reading frame from S. pneumoniae 110K/70, a penicillin-sensitive strain, has been cloned, expressed and purified. Crystals obtained from the purified recombinant enzyme have been obtained in two different forms, which may represent different liganded states, diffracting to 2.7 and 1.5 Å, respectively.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 362-364  [ doi:10.1107/S090744490302777X ]

Purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum

M.-B. Lascombe, M. Ponchet, L. Cardin, M.-L. Milat, J.-P. Blein and T. Prangé

Synopsis: Sylvaticin, a protein of the elicitin family, has been crystallized by the vapour-diffusion method and diffracts to 2.1 Å resolution.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 365-367  [ doi:10.1107/S0907444903027781 ]

Crystallization and preliminary X-ray crystallographic analysis of a ytfG gene product from Escherichia coli

I.-K. Kim, H.-S. Yim, D.-W. Kim, Y.-M. Kim, H.-S. Lee, S.-S. Cha and S.-O. Kang

Synopsis: The E. coli ytfG gene product, with NAD(P)H:quinone oxidoreductase activity, has been crystallized by the hanging-drop vapour-diffusion method at 296 K.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 368-370  [ doi:10.1107/S0907444903027926 ]

Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF

K. Saikrishnan, S. K. Kalapala, M. Bidya Sagar, A. R. Rao, U. Varshney and M. Vijayan

Synopsis: The ribosome recycling factor from M. tuberculosis has been crystallized and the crystals have been characterized.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 371-373  [ doi:10.1107/S0907444903028002 ]

Purification, crystallization and preliminary X-ray diffraction analysis of the catalytic domain of adenylyl cyclase Rv1625c from Mycobacterium tuberculosis

A. D. Ketkar, A. R. Shenoy, M. M. Kesavulu, S. S. Visweswariah and K. Suguna

Synopsis: A mutant of the catalytic domain of mycobacterial adenylyl cyclase Rv1625c has been overexpressed, purified and crystallized. X-ray diffraction data were collected to 3.4 Å resolution.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 374-375  [ doi:10.1107/S090744490302818X ]

Crystallization and preliminary X-ray crystallographic studies on recombinant rat choline acetyltransferase

W. Lian, Y. Gu, B. Pedersen, T. Kukar, L. Govindasamy, M. Agbandje-McKenna, S. Jin, R. McKenna and D. Wu

Synopsis: Using purified, recombinant rat choline acetyltransferase crystals that diffract X-rays to 1.55 Å resolution were generated.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 376-378  [ doi:10.1107/S0907444903028208 ]

Crystals of the ribonucleotide reductase R2 protein from Chlamydia trachomatis obtained by heavy-atom co-crystallization

P. Stenmark, M. Högbom, C. Roshick, G. McClarty and P. Nordlund

Synopsis: The R2 protein of ribonucleotide reductase from C. trachomatis has been crystallized. Co-crystallization with lead was necessary to obtain crystals.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 379-381  [ doi:10.1107/S0907444903028191 ]

Crystallization and preliminary X-ray crystallographic analysis of the RecR protein from Deinococcus radiodurans, a member of the RecFOR DNA-repair pathway

B. I. Lee, K. H. Kim, S. M. Shim, K. S. Ha, J. K. Yang, H.-J. Yoon, J. Y. Ha and S. W. Suh

Synopsis: RecR from D. radiodurans has been crystallized (space group C222₁; unit-cell parameters a = 106.96, b = 122.25, c = 156.01 Å). Diffraction data have been collected to 2.90 Å using Cu K X-rays.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 382-384  [ doi:10.1107/S090744490302821X ]

Crystallization and preliminary X-ray crystallographic analyses of CMY-1 and CMY-10, plasmidic class C -lactamases with extended substrate spectrum

S.-J. Lee, J. Y. Kim, H. I. Jung, P.-G. Suh, H.-S. Lee, S. H. Lee and S.-S. Cha

Synopsis: CMY-1 and CMY-10, the plasmid-encoded class C -lactamases with extended substrate spectrum, were purified and crystallized.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 385-387  [ doi:10.1107/S0907444903028373 ]

Crystallization and preliminary X-ray analysis of an acetone carboxylase from Xanthobacter autotrophicus strain Py2

B. Nocek, J. Boyd, S. A. Ensign and J. W. Peters

Synopsis: The unique carboxylating enzyme acetone carboxylase from X. autotropicus strain Py2 has been crystallized in the native state and 3.2 Å resolution data have been collected.

Online 24 January 2004

 

Acta Cryst. (2004). D60, 388-391  [ doi:10.1107/S0907444903028506 ]

Crystallization of 4-hydroxybenzoyl-CoA reductase and the structure of its electron donor ferredoxin

M. Unciuleac, M. Boll, E. Warkentin and U. Ermler

Synopsis: 4-Hydroxybenzoyl-CoA reductase from Thauera aromatica and its electron donor ferredoxin were anaerobically crystallized. The structure of the ferredoxin was solved at 2.9 Å resolution.

PDB reference: 1rgv

Online 24 January 2004

 

Acta Cryst. (2004). D60, 392-396  [ doi:10.1107/S0907444903027410 ]

Structural analysis of neprilysin with various specific and potent inhibitors

C. Oefner, B. P. Roques, M.-C. Fournie-Zaluski and G. E. Dale

Synopsis: The crystal structures of the soluble extracellular domain of human neutral endopeptidase (residues 52-749) complexed with various potent and competitive inhibitors are described.

PDB references: 1r1h, 1r1i and 1r1j

Online 24 January 2004

 

Acta Cryst. (2004). D60, 397-400  [ doi:10.1107/S0907444903027999 ]

Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 Å resolution suggests a mechanism for stereocontrol during catalysis

A. J. Lloyd, T. Huyton, J. Turkenburg and D. I. Roper

Synopsis: The crystal structure of diaminopimelate epimerase has been refined to 1.75 Å, highlighting differences from the previously determined structure and enabling mechanistic deductions and comparisons with the functionally related amino-acid racemases to be made.

PDB reference: 1gqz

Online 24 January 2004

    

Acta Cryst. (2004). D60, 401-403  [ doi:10.1107/S0907444903028439 ]

Structure of the saccharide-binding domain of the human natural killer cell inhibitory receptor p75/AIRM1

N. Dimasi, A. Moretta, L. Moretta, R. Biassoni and R. A. Mariuzza

Synopsis: p75/AIRM1, also known as Siglec-7, is a sialoadhesin expressed on natural killer cells that is able to inhibit their cytolytic activity. The X-ray crystal structure of the extracellular IgV-like domain, thought to be involved in target-cell recognition, has been determined at higher resolution (1.45 Å) and in a different space group to the previously reported Siglec-7 structure.

PDB reference: 1nko

Online 24 January 2004

 

Acta Cryst. (2004). D60, 404  [ doi:10.1107/S0907444904001283 ]

Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure. 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, 90-96.

Online 24 January 2004