Biological Crystallography

 

Acta Cryst. (2003). D59, 1347-1356  [ doi:10.1107/S0907444903011107 ]

Morphology and the strength of intermolecular contacts in protein crystals

Y. Matsuura and A. A. Chernov

Synopsis: The strengths of intermolecular contacts were calculated for polymorphous lysozyme crystals. The surface energies were calculated to correlate with morphology.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1357-1365  [ doi:10.1107/S0907444903011144 ]

The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features

I. Leiros, E. Moe, O. Lanes, A. O. Smalås and N. P. Willassen

Synopsis: The crystal structure of cod uracil-DNA glycosylase determined at 1.9  Å resolution reveals a decreased number of ion-pair interactions, a less optimally packed core and an optimization of the electrostatic surface potential of the DNA-binding regions compared with the human counterpart.

PDB reference: 1okb

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1366-1370  [ doi:10.1107/S0907444903011156 ]

Crystal structure of -luffin, a ribosome-inactivating protein, at 2.0  Å resolution

Q. Ma, J. Li, H. Li, S. Wu and Y. Dong

Synopsis: The crystal structure of -luffin at 2.0  Å resolution has been solved by the molecular-replacement method using polyalanyl trichosanthin as the search model.

PDB reference: 1nio

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1371-1376  [ doi:10.1107/S0907444903011247 ]

Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom

J. A. Kovacs, P. Chacón, Y. Cong, E. Metwally and W. Wriggers

Synopsis: The three-dimensional `fast rotational matching' method is extended to the full six-dimensional (rotation and translation) matching scenario between two three-dimensional objects. The approach allows treatment of five of the six degrees of freedom by means of fast Fourier transforms.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1377-1383  [ doi:10.1107/S0907444903011788 ]

Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5  Å resolution

K. Shi, B. Pan and M. Sundaralingam

Synopsis: The crystal structure of a DNA/RNA chimera (dC)(rC)d(ATCG) complexed with daunomycin adopts the B-form helical conformation, similar to the DNA counterpart duplex. A model of B-form RNA duplex has been suggested, in which the interaction of the 2'-hydroxyl groups depends on their 3'-side nucleotide.

PDB reference: 1jo2

NDB reference: DD0041

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1384-1394  [ doi:10.1107/S090744490301165X ]

Lessons from an aged, dried crystal of T₆ human insulin

G. D. Smith and R. H. Blessing

Synopsis: In the absence of an ordered water structure in a crystal air-dried at room temperature, the N-termini of the A chains undergo partial unfolding. Both at room temperature and at 100  K, the majority of the GluB13 side chains in the central core of the hexamer in the air-dried crystal are disordered.

PDB references: 1os3 and 1os4

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1395-1407  [ doi:10.1107/S0907444903011880 ]

Structure of the histone-core octamer in KCl/phosphate crystals at 2.15  Å resolution

L. Chantalat, J. M. Nicholson, S. J. Lambert, A. J. Reid, M. J. Donovan, C. D. Reynolds, C. M. Wood and J. P. Baldwin

Synopsis: The structure of the histone-core octamer crystallized in KCl/phosphate compares well with the octamer in the nucleosome but exhibits unique inter-octamer crystal-packing interactions.

PDB reference: 1hq3

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1408-1413  [ doi:10.1107/S0907444903011867 ]

A manual nanoscale method for protein crystallization

J. I. Yeh

Synopsis: A method for manual crystallization using nanolitre volumes is reported.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1414-1421  [ doi:10.1107/S0907444903011831 ]

Structure of MrsD, an FAD-binding protein of the HFCD family

M. Blaesse, T. Kupke, R. Huber and S. Steinbacher

Synopsis: The structure of the LanD protein MrsD at 2.54  Å is described.

PDB reference: 1p3y

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1422-1428  [ doi:10.1107/S0907444903011909 ]

The influence of detergents and amphiphiles on the solubility of the light-harvesting I complex

M. A. Rosenow, D. Brune and J. P. Allen

Synopsis: The light-harvesting I complex was found to be most soluble in detergent and amphiphile combinations that also yielded protein crystals. Amphiphiles that were effective for crystallization were found by mass spectrometry to displace bound detergent.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1429-1434  [ doi:10.1107/S0907444903012526 ]

SAD phasing with triiodide, softer X-rays and some help from radiation damage

G. Evans, M. Polentarutti, K. Djinovic Carugo and G. Bricogne

Synopsis: Low-redundancy SAD data recorded at = 2.0  Å on a triiodide derivative of porcine pancreatic elastase shows evidence of radiation damage at iodine heavy-atom sites which can be used very simply within SHARP to enhance the phasing signal.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1435-1439  [ doi:10.1107/S0907444903012538 ]

Phasing protein structures using the group-subgroup relation

L. Di Costanzo, F. Forneris, S. Geremia and L. Randaccio

Synopsis: The structures of two crystal forms of a four-helix bundle protein have been solved using group-subgroup relations between space groups of polymorphic protein crystals.

PDB references: 1ovu and 1ovv

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1440-1446  [ doi:10.1107/S090744490301254X ]

A practical phasing procedure using the MAD method without the aid of XAFS measurements: successful solution in the structure determination of the outer-membrane lipoprotein carrier LolA

K. Takeda, H. Miyatake, N. Yokota, S. Matsuyama, H. Tokuda and K. Miki

Synopsis: A practical procedure for MAD phasing was successfully performed without the aid of XAFS measurements to solve the crystal structure of the outer-membrane lipoprotein carrier LolA from E. coli.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1447-1453  [ doi:10.1107/S0907444903012629 ]

Structure of xylanase Xys1 from Streptomyces halstedii

A. Canals, M. C. Vega, F. X. Gomis-Rüth, M. Díaz, R. I. Santamaría and M. Coll

Synopsis: The three-dimensional structure of the catalytic domain is reported at 1.78  Å resolution, showing a (/)₈ barrel fold, and compared with related xylanases.

PDB reference: 1nq6

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1454-1458  [ doi:10.1107/S0907444903013192 ]

Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida

B. J. Bell, L. Watanabe, J. L. Rios-Steiner, A. Tulinsky, L. Lebioda and R. K. Arni

Synopsis: The crystal structure of trimeric KDPG aldolase from P. putida, a Class I Schiff-base forming enzyme in the Entner-Doudoroff pathway, is described.

PDB reference: 1mxs

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1459-1461  [ doi:10.1107/S0907444903011521 ]

Crystallization and preliminary X-ray analysis of a four-copper laccase from Coriolus hirsutus

T. V. Pegasova, P. Zwart, O. V. Koroleva, E. V. Stepanova, D. V. Rebrikov and V. S. Lamzin

Synopsis: A four-copper-containing laccase from C. hirsutus was crystallized. The data were collected to 1.85  Å resolution and initial phases have been obtained using the SAD method.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1462-1463  [ doi:10.1107/S0907444903011004 ]

Crystallization and preliminary crystallographic studies on the extrinsic 23  kDa protein in the oxygen-evolving complex of photosystem II

K. Ifuku, T. Nakatsu, H. Kato and F. Sato

Synopsis: The extrinsic protein in an oxygen-evolving complex (OEC23) of photosystem II, tobacco OEC23, was crystallized by the hanging-drop vapour-diffusion technique with PEG 4000 and diffraction data were collected to 2.0  Å.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1464-1465  [ doi:10.1107/S0907444903011314 ]

Crystallization and preliminary X-ray analysis of LC3-I

K. Sugawara, N. N. Suzuki, Y. Fujioka, N. Mizushima, Y. Ohsumi and F. Inagaki

Synopsis: LC3, a protein involved in autophagy in mammalian cells, was crystallized. A complete diffraction data set was collected to a resolution limit of 2.1  Å.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1466-1468  [ doi:10.1107/S0907444903010990 ]

Crystallization and preliminary structure determination of the C-terminal truncated domain of the S-layer protein SbsC

T. Pavkov, M. Oberer, E. M. Egelseer, M. Sára, U. B. Sleytr and W. Keller

Synopsis: Crystals of the C-terminal truncated domain of the S-layer protein SbsC from G. stearothermophilus have been obtained. Diffraction data were collected to a resolution of 3.0  Å from a native crystal and to 3.2  Å from a Pt derivative.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1469-1471  [ doi:10.1107/S0907444903011090 ]

Crystallization and preliminary X-ray diffraction studies of the glutathione S-transferase from Plasmodium falciparum

C. Burmeister, M. Perbandt, Ch. Betzel, R. D. Walter and E. Liebau

Synopsis: Glutathione S-transferase from the human malarial parasite P. falciparum has been crystallized, allowing its X-ray structure determination.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1472-1473  [ doi:10.1107/S0907444903011405 ]

Crystallization and preliminary X-ray diffraction data for the carboxylesterase Est30 from Bacillus stearothermophilus

P. Liu, Y.-F. Wang, H. E. Ewis, A. Abdelal, C. D. Lu and I. T. Weber

Synopsis: The carboxylesterase Est30 from B. stearothermophilus has been crystallized in space group C222₁, with unit-cell parameters a = 55.83, b = 58.15, c = 179.65  Å. The crystal diffracted to better than 2.0  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1474-1476  [ doi:10.1107/S0907444903011326 ]

Crystallization and preliminary X-ray crystallographic studies of mavicyanin from Cucurbita pepo medullosa

Y. Xie, T. Inoue, Y. Miyamoto, H. Matsumura, K. Kataoka, K. Yamaguchi, S. Suzuki and Y. Kai

Synopsis: Recombinant protein mavicyanin from C. pepo medullosa, which is a member of the phytocyanin subclass of cupredoxins was crystallizaed and its preliminary crystallographic data were reported.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1477-1478  [ doi:10.1107/S0907444903011533 ]

Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2

N. N. Suzuki, K. Koizumi, M. Fukushima, A. Matsuda and F. Inagaki

Synopsis: Human uridine-cytidine kinase 2 alone or in complex with ligands crystallized in six crystal forms. One form diffracted to 1.8  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1479-1480  [ doi:10.1107/S0907444903011636 ]

Crystallization and preliminary crystallographic analysis of the autoinhibited form of the tandem SH3 domain of p47^phox

S. Yuzawa, N. N. Suzuki, Y. Fujioka, K. Ogura, H. Sumimoto and F. Inagaki

Synopsis: An autoinhibited form of the tandem SH3 domain of p47^phox, phagocyte NADPH oxidase regulatory component, has been crystallized and X-ray diffraction data have been collected to 2.1  Å resolution using synchrotron radiation.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1481-1483  [ doi:10.1107/S0907444903011648 ]

Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot virus

K.-C. Lee, D. Lim, S.-M. Wong and T. Dokland

Synopsis: The hibiscus chlorotic ringspot virus (HCRSV), a member of the family Tombusviridae, has been purified and subsequently crystallized in space group P23.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1484-1486  [ doi:10.1107/S0907444903011843 ]

Crystallization of FLINC4, an intramolecular LMO4-ldb1 complex

J. E. Deane, M. J. Maher, D. B. Langley, S. C. Graham, J. E. Visvader, J. M. Guss and J. M. Matthews

Synopsis: An intramolecular complex consisting of the interacting domains from two transcriptional regulators, LMO4 and ldb1, has been crystallized. Data were collected to 1.3  Å resolution in addition to MAD data to 1.7  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1487-1489  [ doi:10.1107/S0907444903011879 ]

Crystallization and preliminary X-ray crystallographic studies on the fungal immunomodulatory protein Fve from the golden needle mushroom (Flammulina velutipes)

S. V. Seow, I.-C. Kuo, P. Paaventhan, P. R. Kolatkar and K. Y. Chua

Synopsis: Crystals of the fungal immunomodulatory protein Fve from the edible golden needle mushroom (F. velutipes) have been obtained and diffracted to 1.4  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1490-1492  [ doi:10.1107/S0907444903011855 ]

Crystallization and preliminary X-ray diffraction analysis of KsgA, a universally conserved RNA adenine dimethyltransferase in Escherichia coli

H. C. O'Farrell, F. N. Musayev, J. N. Scarsdale, H. T. Wright and J. P. Rife

Synopsis: KsgA, a ubiquitous rRNA dimethyltransferase, has been crystallized in space group C2, with unit-cell parameters a = 173.9, b = 38.4, c = 83.0  Å, = 90.0°. X-ray data were collected to 1.9  Å with Cu  K radiation.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1493-1495  [ doi:10.1107/S0907444903011910 ]

Crystallization of restriction endonuclease SfiI in complex with DNA

H. Viadiu, É. S. Vanamee, E. M. Jacobson, I. Schildkraut and A. K. Aggarwal

Synopsis: The crystallization of the tetrameric type IIF restriction endonuclease SfiI in complex with DNA is reported.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1496-1498  [ doi:10.1107/S0907444903012289 ]

Purification, crystallization and preliminary X-ray analysis of human pirin

Q. Zeng, X. Li, M. Bartlam, G. Wang, H. Pang and Z. Rao

Synopsis: Human pirin, a novel highly conserved nuclear protein, has been cloned, expressed, purified and crystallized using PEG as precipitant.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1499-1501  [ doi:10.1107/S0907444903012836 ]

Crystallization and preliminary X-ray analysis of alginate lyase, a member of family PL-7, from Pseudomonas aeruginosa

M. Yamasaki, S. Moriwaki, W. Hashimoto, B. Mikami and K. Murata

Synopsis: The crystallization and preliminary X-ray characterization of alginate lyase (family PL-7) from P. aeruginosa are presented.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1502-1503  [ doi:10.1107/S090744490301271X ]

Crystallization and preliminary crystallographic analysis of DJ-1, a protein associated with male fertility and parkinsonism

K. Honbou, N. N. Suzuki, M. Horiuchi, T. Taira, T. Niki, H. Ariga and F. Inagaki

Synopsis: Human DJ-1, a protein associated with male fertility and parkinsonism has been crystallized. A data set was collected to 2.00  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1504-1506  [ doi:10.1107/S0907444903012721 ]

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the structural domain of the nucleocapsid N protein from porcine reproductive and respiratory syndrome virus (PRRSV)

D. N. P. Doan and T. Dokland

Synopsis: The structural domain of the PRRSV nucleocapsid N protein has been expressed in E. coli and crystallized and a complete native data set has been collected at 2.7  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1507-1509  [ doi:10.1107/S0907444903012848 ]

Crystallization and preliminary X-ray studies on the putative dTDP sugar epimerase NovW from the novobiocin biosynthetic cluster of Streptomyces spheroides

P. Jakimowicz, C. L. Freel Meyers, C. T. Walsh, M. J. Buttner and D. M. Lawson

Synopsis: A putative dTDP sugar epimerase (NovW) from S. spheroides, implicated in novobiocin biosynthesis, has been overexpressed in E. coli and purified and crystals diffracting X-rays to 2.0  Å resolution have been obtained.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1510-1513  [ doi:10.1107/S090744490301285X ]

Purification, crystallization and preliminary X-ray analysis of Escherichia coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC)

T. Deva, K. D. Pryor, B. Leiting, E. N. Baker and C. A. Smith

Synopsis: MurC is responsible for the first step in the addition of the pentapeptide unit of peptidoglycan. Native and SeMet crystals of the E. coli enzyme have been prepared.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1514-1516  [ doi:10.1107/S0907444903012964 ]

Crystallization and preliminary X-ray characterization of the relaxase domain of F factor TraI

C. Larkin, S. Datta, A. Nezami, J. A. Dohm and J. F. Schildbach

Synopsis: The 36  kDa relaxase domain of the TraI protein of conjugative plasmid F factor has been crystallized by the sitting-drop method in native and selenomethionine-substituted forms. Data sets from trigonal crystals have been collected to 2.5  Å resolution for the native protein and to 3.1  Å resolution for the selenomethionine protein.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1517-1520  [ doi:10.1107/S0907444903013428 ]

Expression, purification, crystallization and preliminary X-ray analysis of phosphotransacetylase from Methanosarcina thermophila

P. P. Iyer, S. H. Lawrence, H. P. Yennawar and J. G. Ferry

Synopsis: Phosphotransacetylase has been crystallized for the first time. The enzyme from M. thermophila was crystallized in space group I4₁, with unit-cell parameters a = b = 114.8, c = 127.8  Å, = = = 90°; the crystals diffracted to 2.5  Å resolution.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1521-1524  [ doi:10.1107/S0907444903011338 ]

U1A RNA-binding domain at 1.8  Å resolution

P. B. Rupert, H. Xiao and A. R. Ferré-D'Amaré

Synopsis: The C-terminal helix involved in RNA binding has been shown to occlude the binding surface in a previous solution structure of a free U1A. A new 1.8  Å resolution structure of the free protein shows the helix in the same location as in an RNA-bound complex.

PDB reference: 1nu4

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1525-1528  [ doi:10.1107/S0907444903012381 ]

Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G]

G. Schuerman, K. Van Hecke and L. Van Meervelt

Synopsis: 5-Iodo-2'-deoxyuridine (IDU) was the first antiviral nucleoside against herpes simplex virus type 1 and type 2. The structure of d[CACG(IDU)G] reveals two cobalt hexammine complexes in binding modes similar to other cobalt hexammine-containing Z-DNA fragments.

PDB reference: 1omk

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1529-1531  [ doi:10.1107/S0907444903013416 ]

-Crustacyanin, the blue-purple carotenoprotein of lobster carapace: consideration of the bathochromic shift of the protein-bound astaxanthin

P. F. Zagalsky

Synopsis: Conformational change and hydrogen bonding of protein-bound astaxanthin are argued to be the predominant factors responsible for the purple-blue colour of the lobster carapace carotenoprotein -crustacyanin. The further shifted visible spectra of carotenoids with a cyclopentenedione ring remain to be accounted for.

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1532  [ doi:10.1107/S090744490301179X ]

Hemoglobin Disorders, Molecular Methods and Protocols

Online 23 July 2003

 

Acta Cryst. (2003). D59, 1532  [ doi:10.1107/S0907444903015890 ]

Linus Pauling selected scientific papers

Online 23 July 2003