Biological Crystallography

 

Acta Cryst. (2002). D58, 1387-1392  [ doi:10.1107/S0907444902010284 ]

Flat bulk-solvent model: obtaining optimal parameters

A. Fokine and A. Urzhumtsev

Synopsis: The parameters of the flat bulk-solvent model have been studied. A procedure for their search is suggested which allows improvement of the correspondence between the calculated and experimental data.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1393-1399  [ doi:10.1107/S0907444902010442 ]

Analysis of quinazoline and pyrido[2,3-d]pyrimidine N9-C10 reversed-bridge antifolates in complex with NADP⁺ and Pneumocystis carinii dihydrofolate reductase

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

Synopsis: The crystal structure studies of two ternary complexes of P. carinii dihydrofolate reductase with the cofactor NADP⁺ and potent antifolates, the N9-C10 reversed-bridge inhibitor 2,4-diamino-6-[N-(2',5'-dimethoxybenzyl)-N-methylamino]quinazoline and its 3',5'-dimethoxypyrido[2,3-d]pyrimidine analog, have been carried out.

PDB references: 1ly3 and 1ly4

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1400-1406  [ doi:10.1107/S0907444902010454 ]

Structure of cyclized green fluorescent protein

A. Hofmann, H. Iwai, S. Hess, A. Plückthun and A. Wlodawer

Synopsis: The crystal structure of cyclized green fluorescent protein (cGFP), which was engineered using split-intein technology, has been refined and shows that the linker does not impose any restraints on the fold. A new mode of dimerization of GFP was observed.

PDB reference: 1kp5

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1407-1412  [ doi:10.1107/S0907444902010934 ]

Metal binding to porcine pancreatic elastase: calcium or not calcium

M. S. Weiss, S. Panjikar, E. Nowak and P. A. Tucker

Synopsis: Orthorhombic crystals of porcine pancreatic elastase have been grown in the presence of sodium sulfate and in the presence of sodium citrate plus calcium chloride. The observed differences in the diffraction patterns lead to the conclusion that elastase in its canonical Na₂SO₄ crystal form does not contain calcium in its metal-binding site but sodium instead.

PDB references: 1lka and 1lkb

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1413-1420  [ doi:10.1107/S0907444902011010 ]

Xenon derivatization of halide-soaked protein crystals

S. Panjikar and P. A. Tucker

Synopsis: Crystals derived by soaking in bromide solutions can subsequently be derived under a xenon atmosphere. Intensity data collected to lower energy than the bromine absorption edge can be used to determine the xenon position and the resultant phase information used to determine the bromine substructure from data collected to higher energy than the bromine absorption edge.

PDB references: 1l0z and 1l1g

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1421-1432  [ doi:10.1107/S0907444902011277 ]

Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors

Y. Joti, M. Nakasako, A. Kidera and N. Go

Synopsis: Crystallographic normal-mode refinement was carried out for the diffraction data of human lysozyme obtained at temperatures ranging from 113 to 178  K. The effects of a dynamic transition that occurred at about 150  K on the dynamic structures as well as the static structures of a protein molecule in a crystal are discussed.

PDB references: 1iwt, 1iwu, 1iwv, 1iww, 1iwx, 1iwy and 1iwz

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1433-1441  [ doi:10.1107/S0907444902011368 ]

Advantages of high-resolution phasing: MAD to atomic resolution

A. Schmidt, A. Gonzalez, R. J. Morris, M. Costabel, P. M. Alzari and V. S. Lamzin

Synopsis: The structure of the endoglucanase A from Clostridium thermocellum CelA has been re-solved by three-wavelength MAD.

PDB reference: 1is9

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1442-1447  [ doi:10.1107/S0907444902011745 ]

The 1.45  Å resolution structure of the cryptogein-cholesterol complex: a close-up view of a sterol carrier protein (SCP) active site

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

Synopsis: The phytotoxic cryptogein, a 10  kDa protein from an oomycete fungus, gives a cholesterol complex at high resolution.

PDB reference: 1lri

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1448-1461  [ doi:10.1107/S0907444902011769 ]

Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination

R. Thaimattam, E. Tykarska, A. Bierzynski, G. M. Sheldrick and M. Jaskolski

Synopsis: The 1  Å resolution structure of a mutant of trypsin inhibitor from squash reveals a 4:1 protein-zinc complex with unusual coordination.

PDB reference: 1lu0

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1462-1464  [ doi:10.1107/S0907444902008429 ]

Adenovirus proteinase: crystallization and preliminary X-ray diffraction studies to atomic resolution

M. L. Baniecki, W. J. McGrath, Z. Dauter and W. F. Mangel

Synopsis: Comparison of the structure of the adenovirus proteinase, whose crystallization and X-ray diffraction are reported here, with that of the enzyme activated by the 11-amino acid peptide pVIc will reveal why the enzyme is inactive and how the enzyme is activated by pVIc. The low solvent content, 29.2%, may be the reason why this crystal diffracted to such high resolution, 0.98  Å.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1465-1466  [ doi:10.1107/S0907444902010302 ]

Crystallization and preliminary X-ray studies of cold-active protein-tyrosine phosphatase of Shewanella sp.

H. Tsuruta, B. Mikami, C. Yamamoto and Y. Aizono

Synopsis: Cold-active protein-tyrosine phosphatase of a psychrophile, Shewanella sp., has beencrystallized and the diffraction data were collected using Cu  K X-ray radiation.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1467-1469  [ doi:10.1107/S0907444902010570 ]

Crystallization and preliminary X-ray diffraction studies of the peptide methionine sulfoxide reductase B domain of Neisseria meningitidis PILB

B. Kauffmann, F. Favier, A. Olry, S. Boschi-Muller, P. Carpentier, G. Branlant and A. Aubry

Synopsis: Peptide methionine sulfoxide reductase B from N. meningitidis and its selenomethionine-substituted form were crystallized. A MAD experiment was performed at 1.8  Å resolution and an electron-density map of excellent quality was obtained from the resulting phases.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1470-1473  [ doi:10.1107/S0907444902010685 ]

Crystallization and preliminary X-ray analysis of an R-2-hydroxypropyl-coenzyme M dehydrogenase

B. Nocek, D. D. Clark, S. A. Ensign and J. W. Peters

Synopsis: The R-2-hydroxypropyl-coenzyme M dehydrogenase has been crystallized in the presence and absence of its reaction substrates and 1.90  Å resolution data have been collected.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1474-1475  [ doi:10.1107/S0907444902010909 ]

Isolation, purification and preliminary X-ray characterization of Cpn60-2 (65  kDa heat-shock protein) from Mycobacterium tuberculosis

N. Adir, E. Dobrovetsky, I. Shafat, C. Cohen and Y. Kashi

Synopsis: The 65  kDa heat-shock protein (Cpn60-2) from M. tuberculosis has been crystallized and its preliminary crystallographic characterization is reported.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1476-1478  [ doi:10.1107/S0907444902010922 ]

Preliminary X-ray crystallographic analysis of a soluble form of MntC, a periplasmic manganese-binding component of an ABC-type Mn transporter from Synechocystis sp. PCC 6803

N. Adir, V. Rukhman, B. Brumshtein and R. Anati

Synopsis: Crystallization and preliminary crystallographic study of the MntC manganese-binding protein, the solute-binding component of an ABC transport system from Synechocytis sp. PCC 6803, is reported.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1479-1481  [ doi:10.1107/S0907444902011034 ]

Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain

M.-H. Li, F. Kwok, X.-M. An, W.-R. Chang, C.-K. Lau, J.-P. Zhang, S.-Q. Liu, Y.-C. Leung, T. Jiang and D.-C. Liang

Synopsis: Pyridoxal kinase from sheep brain has been crystallized in space group P2₁2₁2₁; the crystals diffract to 2.1  Å. Two heavy-atom derivatives have been prepared.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1482-1483  [ doi:10.1107/S0907444902011046 ]

Crystallization and preliminary crystallographic analysis of a D-aminoacylase from Alcaligenes faecalis DA1

C.-S. Hsu, S.-J. Chen, Y.-C. Tsai, T.-W. Lin, S.-H. Liaw and A.H.-J. Wang

Synopsis: The first D-aminoacylase crystal from A. faecalis has been obtained in hanging drops at pH 5.6 by the vapour-diffusion method using 30% polyethylene glycol 4000 as precipitant.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1484-1486  [ doi:10.1107/S0907444902012969 ]

Crystallization and preliminary crystallographic study of a ternary complex between the T4 phage -glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site

L. Larivière, J. Kurzeck, U. Aschke-Sonnenborn, W. Rüger and S. Moréra

Synopsis: T4 phage -glucosyltransferase has been crystallized with an abasic site-containing DNA and uridine diphosphoglucose to investigate a base-flipping phenomenon.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1487-1489  [ doi:10.1107/S0907444902011563 ]

Crystallization and preliminary X-ray diffraction studies of the complete modular endolysin from Cp-1, a phage infecting Streptococcus pneumoniae

B. Monterroso, A. Albert, M. Martínez-Ripoll, P. García, J. L. García, M. Menéndez and J. A. Hermoso

Synopsis: The endolysin coded by the phage Cp-1 has been crystallized by the hanging-drop vapour-diffusion method and by addition of a specific detergent. Native data have been collected to 2.1  Å resolution.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1490-1493  [ doi:10.1107/S0907444902011575 ]

Spore-coat laccase CotA from Bacillus subtilis: crystallization and preliminary X-ray characterization by the MAD method

F. J. Enguita, P. M. Matias, L. O. Martins, D. Plácido, A. O. Henriques and M. A. Carrondo

Synopsis: The crystallization of a recombinant CotA protein produced in E. coli and the preliminary characterization of the crystals is reported

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1494-1496  [ doi:10.1107/S0907444902011666 ]

Crystallization and preliminary X-ray analysis of a xylanase from the psychrophile Pseudoalteromonas haloplanktis

F. Van Petegem, T. Collins, M.-A. Meuwis, C. Gerday, G. Feller and J. Van Beeumen

Synopsis: Crystals were obtained of a cold-adapted xylanase and both native data and SAD data from a SeMet-substituted enzyme were collected.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1497-1500  [ doi:10.1107/S0907444902011770 ]

Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus

M. N. Vassylyeva, J. Lee, S. Sekine, O. Laptenko, S. Kuramitsu, T. Shibata, Y. Inoue, S. Borukhov, D. G. Vassylyev and S. Yokoyama

Synopsis: Bacterial RNA polymerase holoenzyme, an assembly of six protein subunits with a total molecular mass of 450  kDa, was crystallized under near-physiological conditions. A complete diffraction data set was collected at 3  Å resolution. The structure determination and refinement is in progress.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1501-1503  [ doi:10.1107/S0907444902011782 ]

Crystallization and preliminary X-ray data of a bifunctional peroxiredoxin from poplar

A. Echalier, C. Corbier, N. Rouhier, J.-P. Jacquot and A. Aubry

Synopsis: The wild-type peroxiredoxin from poplar and the V152C mutated protein have been crystallized. Native data sets, X-ray analyses and a molecular-replacement solution are presented.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1504-1506  [ doi:10.1107/S0907444902011794 ]

Cloning, purification, crystallization and preliminary X-ray analysis of DOS heme domain, a new heme oxygen sensor in Escherichia coli

H. Park, C. Suquet, M. I. Savenkova, J. D. Satterlee and C. Kang

Synopsis: The direct oxygen sensor (DOSH) protein from E. coli is uniquely six-coordinate in both ferric and ferrous heme states and the oxidized form of this protein has been crystallized.

Online 23 August 2002

 

Acta Cryst. (2002). D58, 1507-1510  [ doi:10.1107/S0907444902011885 ]

Crystallization and preliminary X-ray study of recombinant betaine-homocysteine S-methyltransferase from rat liver

B. González, M. A. Pajares, H.-P. Too, F. Garrido, T. L. Blundell and J. Sanz-Aparicio

Synopsis: Betaine-homocysteine S-methyltransferase from rat liver has been purified and crystallized. Diffraction data from native, selenomethionine-labelled and two heavy-atom derivatives have been collected using synchrotron sources.

Online 23 August 2002