Biological Crystallography

 

Acta Cryst. (2003). D59, 783-794  [ doi:10.1107/S0907444903003482 ]

The architecture of the GroEL-GroES-(ADP)₇ chaperonin complex. I. Heptagrammal molecular forms

A. Janner

Synopsis: Splitting the heptameric chains in the GroEL-GroES chaperonin complex into segments gives rise to molecular forms which obey a law of rational indices and which are invariant with respect to scale-rotations with integral entries.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 795-808  [ doi:10.1107/S0907444903003494 ]

The architecture of the GroEL-GroES-(ADP)₇ chaperonin complex. II. Heptagrammal characterization of the folding

A. Janner

Synopsis: The molecular forms of heptameric chain segments of the GroEL-GroES chaperonin complex lead to folding points at form boundaries. Examples are given of such C positions related by integral scale-rotations.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 809-814  [ doi:10.1107/S0907444903003664 ]

Recursive direct phasing with reference-beam diffraction

Q. Shen and J. Wang

Synopsis: A new recursive phasing method has been developed and used to produce an electron-density map of lysozyme, based on a unique phase-occurrence pattern in a triplet-phase data set measured by reference-beam diffraction.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 815-822  [ doi:10.1107/S0907444903004025 ]

Structure of DNA helicase RepA in complex with sulfate at 1.95  Å resolution implicates structural changes to an `open' form

H. Xu, N. Sträter, W. Schröder, C. Böttcher, K. Ludwig and W. Saenger

Synopsis: A new crystal form of the hexameric DNA helicase RepA encoded by plasmid RSF1010 that has sulfate anions bound to the active sites has been determined to 1.95  Å resolution. These structural data together with electron-microscopy studies implicate conformational changes that lead towards an `open' stucture of RepA upon binding of nucleoside 5'-triphosphates.

PDB reference: 1nlf

Online 25 April 2003

 

Acta Cryst. (2003). D59, 823-827  [ doi:10.1107/S0907444903003792 ]

An evaluation of automated model-building procedures for protein crystallography

J. Badger

Synopsis: A database of 41 experimentally phased electron-density maps between 1.3 and 2.9  Å resolution was used to evaluate the performance of the automated protein model-building procedures within the ARP/wARP, MAID and RESOLVE programs.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 828-834  [ doi:10.1107/S0907444903004153 ]

Structural characterization and comparison of RGD cell-adhesion recognition sites engineered into streptavidin

I. Le Trong, T. C. McDevitt, K. E. Nelson, P. S. Stayton and R. E. Stenkamp

Synopsis: Cell-adhesion properties can be engineered into streptavidin by the insertion of selected fibronectin or osteopontin sequences into an external loop. High-resolution crystal structures of two such streptavidins show that the loops further sample the conformations seen in other RGD motifs.

PDB references: 1mm9 and 1moy

Online 25 April 2003

 

Acta Cryst. (2003). D59, 835-842  [ doi:10.1107/S0907444903041441 ]

The structure of glyceraldehyde 3-phosphate dehydrogenase from Alcaligenes xylosoxidans at 1.7  Å resolution

S. V. Antonyuk, R. R. Eady, R. W. Strange and S. S. Hasnain

Synopsis: The structure of a glyceraldehye 3-phosphate dehydrogenase from a denitrifying bacterium has been determined at 1.7  Å resolution. It confirms the essential role of Cys154 in the enzyme's activity.

PDB reference: 1obf

Online 25 April 2003

 

Acta Cryst. (2003). D59, 843-849  [ doi:10.1107/S0907444903004219 ]

The properties of (2F_o - F_c) and (F_o - F_c) electron-density maps at medium-to-high resolutions

A. Minichino, J. Habash, J. Raftery and J. R. Helliwell

Synopsis: The bound water structure in medium-high versus high-resolution protein (F_o - F_c) difference electron-density maps yields more detail than (2F_o - F_c) maps. Tests on truncated resolution cases and `real' data-set cases are examined. Re-refinements at 3.2  Å show distances that can agree with known values but B values that do not agree with known values.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 850-858  [ doi:10.1107/S0907444903004359 ]

Connectivity-based ab initio phasing at different solvent levels

A. Fokine, N. Lunina, V. Lunin and A. Urzhumtsev

Synopsis: Low-resolution ab initio images obtained from crystals of a RNA-protein complex allow the protein and RNA molecules to be seen alone or in complex depending on the diffraction density of the bulk solvent.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 859-867  [ doi:10.1107/S0907444903004700 ]

Structure of the human S100A12-copper complex: implications for host-parasite defence

O. V. Moroz, A. A. Antson, S. J. Grist, N. J. Maitland, G. G. Dodson, K. S. Wilson, E. Lukanidin and I. B. Bronstein

Synopsis: The structure of S100A12, a member of the S100 family of proteins, has been determined in complex with copper at 2.19  Å resolution. Copper binds to the same site that zinc binds to in the structure of S100A7. The data suggest that copper binding may be essential for the function of S100A12 and probably other calgranulins S100A8 and S100A9 in the early immune response.

PDB reference: 1odb

Online 25 April 2003

 

Acta Cryst. (2003). D59, 868-875  [ doi:10.1107/S0907444903005663 ]

SAD manganese in two crystal forms of glucose isomerase

U. A. Ramagopal, M. Dauter and Z. Dauter

Synopsis: Four individual data sets collected at various wavelengths were used for SAD phasing of two crystal forms of glucose isomerase, including one previously undescribed, using the anomalous signal of a single Mn²⁺ ion present in the 44  kDa molecule, which ranged from 1.2 to 0.6%.

PDB reference: 1oad

Online 25 April 2003

 

Acta Cryst. (2003). D59, 876-880  [ doi:10.1107/S0907444903005390 ]

Structure of a constitutively activated RhoA mutant (Q63L) at 1.55  Å resolution

K. Longenecker, P. Read, S.-K. Lin, A. P. Somlyo, R. K. Nakamoto and Z. S. Derewenda

Synopsis: The structure of the GMPPNP-bound constitutively active Q63L mutant of the cytosolic RhoA GTPase was solved at 1.55  Å resolution and refined using anisotropic displacement parameters. The structure is similar to the Val14 mutant and cannot explain the functional differences that are observed in vivo.

PDB reference: 1kmq

Online 25 April 2003

 

Acta Cryst. (2003). D59, 881-886  [ doi:10.1107/S0907444903005699 ]

Characterization of four orthologs of stringent starvation protein A

M. Andrykovitch, K. M. Routzahn, M. Li, Y. Gu, D. S. Waugh and X. Ji

Synopsis: RNA polymerase-associated stringent starvation proteins A from E. coli, Y. pestis, V. cholerae and P. aeruginosa were characterized and X-ray diffraction-quality crystals were obtained for the Y. pestis protein only.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 887-896  [ doi:10.1107/S0907444903003512 ]

Phasing power at the K absorption edge of organic arsenic

P. Retailleau and T. Prangé

Synopsis: The phasing and ab initio structure-determination potential of organic arsenic derivatives have been studied using lysozyme crystals.

PDB reference: 1n4f

Online 25 April 2003

 

Acta Cryst. (2003). D59, 897-902  [ doi:10.1107/S0907444903005870 ]

An orthorhombic form of Escherichia coli aminopeptidase P at 2.4  Å resolution

S. C. Graham, M. Lee, H. C. Freeman and J. M. Guss

Synopsis: The structure of aminopeptidase P from E. coli in the orthorhombic space group C222₁ has six subunits in the asymmetric unit. The molecular structure is compared with those previously reported in hexagonal and tetragonal space groups.

PDB reference: 1m35

Online 25 April 2003

 

Acta Cryst. (2003). D59, 903-909  [ doi:10.1107/S0907444903006516 ]

Zero-dose extrapolation as part of macromolecular synchrotron data reduction

K. Diederichs, S. McSweeney and R. B. G. Ravelli

Synopsis: A computational method to partially correct radiation damage to protein crystals is described and applied to a test data set with a weak anomalous signal. It is shown that the correction results in an enhancement of SAD phases and electron-density maps.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 910-912  [ doi:10.1107/S0907444903004086 ]

A single mutation of restriction endonuclease EcoRII led to a new crystal form that diffracts to 2.1  Å resolution

X. E. Zhou, Y. Wang, M. Reuter, P. Mackeldanz, D. H. Krüger, E. J. Meehan and L. Chen

Synopsis: R88A, a mutant of restriction endonuclease EcoRII, has been crystallized in a different crystal form to that of the wild type. The mutant crystals diffract to 2.1  Å resolution.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 913-915  [ doi:10.1107/S0907444903004037 ]

Crystallization and preliminary X-ray analysis of a family 51 glycoside hydrolase, the -L-arabinofuranosidase from Geobacillus stearothermophilus T-6

K. Hövel, D. Shallom, K. Niefind, T. Baasov, G. Shoham, Y. Shoham and D. Schomburg

Synopsis: This study describes the first crystallization and preliminary X-ray analysis of the -L-arabinofuranosidase from G. stearothermophilus T-6, a family 51 glycoside hydrolase. Purified native and selenomethionine-containing enzymes were crystallized in two different space groups, P2₁ and R3. The R3 crystal form diffracted X-rays to a resolution of 1.8  Å.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 916-918  [ doi:10.1107/S0907444903004116 ]

Crystallization and preliminary crystallographic study of a pheromone-binding protein from the cockroach Leucophaea maderae

A. Lartigue, S. Rivière, R. Brossut, M. Tegoni and C. Cambillau

Synopsis: An antennal protein from the cockroach L. maderae, expressed specifically in the female adult antennae, shares all the hallmarks of the PBP family. It has been expressed as recombinant protein in E. coli periplasm and crystallized by the sitting-drop vapor-diffusion method using a nanodrop dispensing robot.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 919-921  [ doi:10.1107/S090744490300413X ]

Optimization of crystals from nanodrops: crystallization and preliminary crystallographic study of a pheromone-binding protein from the honeybee Apis mellifera L.

A. Lartigue, A. Gruez, L. Briand, J.-C. Pernollet, S. Spinelli, M. Tegoni and C. Cambillau

Synopsis: The crystallization of a PBP from the honeybee antennae expressed as recombinant protein in the yeast P. pastoris is reported. Unique crystals of this PBP have been obtained with the sitting-drop vapor-diffusion method using a nanodrop dispensing robot with a novel optimization procedure.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 922-926  [ doi:10.1107/S0907444903004414 ]

Two-dimensional crystallization of rabbit C-reactive protein monomeric subunits

Y. Wu, H.-W. Wang, S.-R. Ji and S. Sui

Synopsis: Two forms of two-dimensional crystals composed of monomeric CRP have been obtained on negatively charged lipid monolayers: a previously reported form, MI, and a new form, MII.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 927-929  [ doi:10.1107/S0907444903004487 ]

Co-crystallization of the yeast phosphorelay protein YPD1 with the SLN1 response-regulator domain and preliminary X-ray diffraction analysis

L. Chooback and A. H. West

Synopsis: YPD1, a histidine-containing phosphotransfer (HPt) protein, has been co-crystallized with its upstream phosphodonor, the SLN1-R1 response-regulator domain.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 930-932  [ doi:10.1107/S0907444903004554 ]

Crystallization and preliminary X-ray diffraction analysis of ribosomal protein L11 methyltransferase from Thermus thermophilus HB8

T. Kaminishi, H. Sakai, C. Takemoto-Hori, T. Terada, N. Nakagawa, N. Maoka, S. Kuramitsu, M. Shirouzu and S. Yokoyama

Synopsis: Ribosomal protein L11 methyltransferase from T. thermophilus HB8 has been crystallized. X-ray diffraction data were collected to 1.9  Å using synchrotron radiation.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 933-935  [ doi:10.1107/S0907444903004815 ]

Preparation and crystallization of human flap endonuclease FEN-1 in complex with proliferating-cell nuclear antigen, PCNA

S. Sakurai, K. Kitano, K. Okada, K. Hamada, H. Morioka and T. Hakoshima

Synopsis: Human flap endonuclease-1 complexed with proliferating-cell nuclear antigen has been crystallized. A diffraction data set was collected to a resolution of 3.0  Å.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 936-939  [ doi:10.1107/S0907444903002622 ]

Purification, crystallization and preliminary X-ray diffraction studies of a complex between G protein-coupled receptor kinase 2 and G₁₂

D. T. Lodowski, J. F. Barnhill, J. A. Pitcher, W. D. Capel, R. J. Lefkowitz and J. J. G. Tesmer

Synopsis: A complex between G protein-coupled receptor kinase 2 (GRK2) and G₁₂ has been crystallized in space group C2, with unit-cell parameters a = 187.0, b = 72.1, c = 122.0  Å, = 115.2°. Crystals diffract to beyond 3.2  Å spacing with Cu  K radiation.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 940-942  [ doi:10.1107/S0907444903005420 ]

Crystallization of the proline-rich-peptide binding domain of human type I collagen prolyl 4-hydroxylase

M. Pekkala, R. Hieta, P. Kursula, K. I. Kivirikko, R. K. Wierenga and J. Myllyharju

Synopsis: Crystallization studies on the domain of the (I) subunit of human collagen prolyl 4-hydroxylase that binds the proline-rich peptide are described. The crystals obtained diffract to a resolution of better than 3  Å.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 943-945  [ doi:10.1107/S090744490300578X ]

Crystallization and preliminary X-ray diffraction analysis of thermophilic imidase from pig liver

C.-Y. Huang, S.-K. Chiang, Y.-S. Yang and Y.-J. Sun

Synopsis: Crystals of imidase from pig liver have been crystallized in the triclinic P₁ space group and the orthorhombic C222₁ space group.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 946-949  [ doi:10.1107/S0907444903005912 ]

Crystallization and preliminary X-ray analysis of a novel unsaturated glucuronyl hydrolase from Bacillus sp. GL1

S. Mori, S. Akao, O. Miyake, H. Nankai, W. Hashimoto, B. Mikami and K. Murata

Synopsis: The crystallization and preliminary characterization of unsaturated glucuronyl hydrolase from Bacillus sp. GL1 are presented.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 950-952  [ doi:10.1107/S0907444903005936 ]

Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase

Y.-H. Hsu, C.-Y. Hu, J.-J. Lin and S.-H. Liaw

Synopsis: A recombinant yeast cytosine deaminase has been crystallized, showing diffraction beyond 1.5  Å resolution, and an initial atomic model has been built.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 953-954  [ doi:10.1107/S0907444903006498 ]

Crystallization and preliminary X-ray crystallographic analysis of D-phenylglycine aminotransferase from Pseudomonas stutzeri ST201

P. Kongsaeree, C. Samanchart, P. Laowanapiban, S. Wiyakrutta and V. Meevootisom

Synopsis: D-Phenylglycine aminotransferase from P. stutzeri has been crystallized in the trigonal space group P3₁21 or P3₂21. A 2.3  Å resolution diffraction data set was collected.

Online 25 April 2003

 

Acta Cryst. (2003). D59, 955-957  [ doi:10.1107/S0907444903003597 ]

Structure of a single-chain Fv fragment of an antibody that inhibits the HIV-1 and HIV-2 proteases

J. Lescar, J. Brynda, M. Fabry, M. Horejsi, P. Rezacova, J. Sedlacek and G. A. Bentley

Synopsis: The crystal structure of the single-chain Fv fragment of the monoclonal antibody 1696, which inhibits the protease of HIV-1 and HIV-2, has been determined in the non-complexed state at 1.7  Å resolution. It is compared with the previously determined structures of the non-complexed Fab1696 and scFv1696 as an antibody-antigen complex.

PDB reference: 1n4x

Online 25 April 2003

 

Acta Cryst. (2003). D59, 958  [ doi:10.1107/S0907444903006735 ]

Outline of Crystallography for Biologists

Online 25 April 2003