Biological Crystallography

 

Acta Cryst. (2002). D58, 571-578  [ doi:10.1107/S0907444902001191 ]

Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit -sheets

S. Wang, C. Mura, M. R. Sawaya, D. Cascio and D. Eisenberg

Synopsis: The crystal structure of a Nudix protein from the hyperthermophile P. aerophilum was determined using the single-wavelength anomalous scattering method. An analysis of the structure in terms of putative catalytic function and thermostability is presented.

PDB references: 1jrk, 1k26 and 1k2e

Online 22 March 2002

 

Acta Cryst. (2002). D58, 579-584  [ doi:10.1107/S090744490200121X ]

Synchrotron white-beam X-ray topography of ribonuclease S crystals

W. M. Vetter, D. T. Gallagher and M. Dudley

Synopsis: Experimental conditions for the white-beam topography of ribonuclease S crystals were optimized by considering calculated parameters. Images showing some dynamical contrast were thus obtained with minimal radiation damage to the crystals.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 585-590  [ doi:10.1107/S0907444902001257 ]

Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16  Å resolution

D. M. F. van Aalten, W. Crielaard, K. J. Hellingwerf and L. Joshua-Tor

Synopsis: The crystal structure of photoactive yellow protein with a modified chromophore shows the chromophore to be bound in two different conformations. From this crystallographic study and spectroscopic studies, caffeic acid binds the protein in a strained conformation.

PDB reference: 1kou

Online 22 March 2002

 

Acta Cryst. (2002). D58, 591-600  [ doi:10.1107/S0907444902001567 ]

A structural double-mutant cycle: estimating the strength of a buried salt bridge in barnase

C. K. Vaughan, P. Harryson, A. M. Buckle and A. R. Fersht

Synopsis: A structural and energetic analysis of single and double salt-bridge mutants in barnase reinforces the validity of the double-mutant cycle method used to estimate the strength and cooperativity of molecular interactions in proteins.

PDB references: 1b20, 1b21, 1b2z and 1b2x

Online 22 March 2002

 

Acta Cryst. (2002). D58, 601-606  [ doi:10.1107/S0907444902001889 ]

Structure of the 1:1 netropsin-decamer d(CCIICICCII)₂ complex with a single bound netropsin

K. Shi, S. N. Mitra and M. Sundaralingam

Synopsis: Crystal structure of the netropsin-d(CCIICICCII)₂ shows a preference of netropsin binding to the target DNA. The conformation differences between the drug-binding and the drug-free portions of the DNA are described.

NDB reference: dd0024

Online 22 March 2002

 

Acta Cryst. (2002). D58, 607-614  [ doi:10.1107/S0907444902002135 ]

Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals

T. Ursby, M. Weik, E. Fioravanti, M. Delarue, M. Goeldner and D. Bourgeois

Synopsis: Caged ATP was successfully photolyzed at 100-150  K in crystals of thymidylate kinase as assessed by the structural observation of ATP-dependent enzymatic activity. Cryophotolysis of caged compounds, in combination with the use of adequate temperature profiles, opens new possibilities for trapping intermediate states in protein crystals.

PDB references: 1gsi and 1gtv

Online 22 March 2002

 

Acta Cryst. (2002). D58, 615-621  [ doi:10.1107/S0907444902003189 ]

Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences

N. H. Hopcroft, A. L. Wendt, P. Gollnick and A. A. Antson

Synopsis: X-ray structures of TRAP bound to 53-nucleotide single-stranded RNA containing GAGUU and GAGCC repeats were determined. Comparison of these structures with that of TRAP bound to RNAs containing GAGAU repeats gives insight into the specificity of the TRAP-RNA interaction and suggests that pyrimidine spacer nucleotides bind more strongly owing to the greater increase in entropy upon binding.

PDB references: 1gtf and 1gtn

Online 22 March 2002

 

Acta Cryst. (2002). D58, 622-626  [ doi:10.1107/S0907444902002378 ]

The structure of human recombinant aldose reductase complexed with the potent inhibitor zenarestat

T. Kinoshita, H. Miyake, T. Fujii, S. Takakura and T. Goto

Synopsis: The crystal structure of the complex of human recombinant aldose reductase with zenarestat has been solved at 2.5  Å resolution. Zenarestat fits in the hydrophobic active site and induces unique and dramatic conformational changes.

PDB reference: 1iei

Online 22 March 2002

 

Acta Cryst. (2002). D58, 627-633  [ doi:10.1107/S090744490200255X ]

Structure of an RNase-related protein from Calystegia sepium

A. Rabijns, C. Verboven, P. Rougé, A. Barre, E. J. M. Van Damme, W. J. Peumans and C. De Ranter

Synopsis: The structure of the RNase-related protein from C. sepium explains its complete lack of ribonuclease activity.

PDB reference: 1jy5

Online 22 March 2002

 

Acta Cryst. (2002). D58, 634-644  [ doi:10.1107/S0907444902002627 ]

X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites

M. K. Safo, T. Boyiri, J. C. Burnett, R. Danso-Danquah, C. M. Moure, G. S. Joshi and D. J. Abraham

Synopsis: The rational design and X-ray crystallographic analyses of two symmetrical allosteric effectors of hemoglobin are reported. Both compounds were found to span and link primary and secondary allosteric sites.

PDB reference: 1k0y

Online 22 March 2002

 

Acta Cryst. (2002). D58, 645-652  [ doi:10.1107/S0907444902003177 ]

Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination

J. D. Ng, C. Sauter, B. Lorber, N. Kirkland, J. Arnez and R. Giegé

Synopsis: A comparative crystallographic analysis of earth-grown and space-grown crystals of AspRS-1, a large dimeric enzyme having flexible domains, shows that the latter are of enhanced quality. Their mosaicity as well as the electron-density map and the structure model derived from them are improved.

PDB reference: 1l0w

Online 22 March 2002

 

Acta Cryst. (2002). D58, 653-659  [ doi:10.1107/S0907444902002366 ]

Structure of an endoglucanase from termite, Nasutitermes takasagoensis

S. Khademi, L. A. Guarino, H. Watanabe, G. Tokuda and E. F. Meyer

Synopsis: The first crystal structure of an endo--1,4-glucanase from higher termites refined to 1.4  Å resolution is reported here. The effects of pH changes on the structure of the enzyme are minimal: a structural Ca²⁺ ion is lost at pH 2.5.

PDB references: 1ks8, 1ksc and 1ksd

Online 22 March 2002

 

Acta Cryst. (2002). D58, 660-667  [ doi:10.1107/S0907444902003360 ]

Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride

S. Khademi, D. Zhang, S. M. Swanson, A. Wartenberg, K. Witte and E. F. Meyer

Synopsis: The structure of an endoglucanase from A. niger (EglA) has been determined at 2.1  Å resolution. The mode of inhibition of EglA by palladium chloride was studied by determination of the structure of an EglA-palladium complex.

PDB references: 1ks4 and 1ks5

Online 22 March 2002

 

Acta Cryst. (2002). D58, 668-671  [ doi:10.1107/S0907444902002007 ]

Crystallization and preliminary X-ray study of an N-terminal fragment of rat liver ribosomal P2 protein

D. Mandelman, P. Gonzalo, J.-P. Lavergne, C. Corbier, J.-P. Reboud and R. Haser

Synopsis: The highly soluble domain (1-65) of rat liver P2 has been overexpressed in Escherichia coli as an N-terminal poly-His-tagged protein and crystallized.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 672-674  [ doi:10.1107/S0907444902003840 ]

Crystallization and preliminary X-ray analysis of the complex of porcine pancreatic elastase and a hybrid squash inhibitor

K. Hilpert, J. Schneider-Mergener and J. Aÿ

Synopsis: Porcine pancreatic elastase (EC 3.4.21.36) was crystallized in complex with a chemically synthesized hybrid squash inhibitor. The optimization of crystallization conditions is described.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 675-678  [ doi:10.1107/S0907444902001294 ]

Purification, crystallization and preliminary X-ray crystallographic analysis of agkaggregin, a C-type lectin-like protein from Agkistrodon acutus venom

S. Liu, Z. Zhu, J. Sun, Z. Zhu, Q. Huang, M. Teng and L. Niu

Synopsis: Purification, crystallization and preliminary X-ray crystallographic analysis of a C-type lectin-like protein from A. acutus venom.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 679-682  [ doi:10.1107/S0907444902001397 ]

Crystallization and preliminary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA

K. Pereira de Jésus, L. Serre, N. Hervouet, V. Bouckson-Castaing, C. Zelwer and B. Castaing

Synopsis: Experimental strategies for crystallizing a non-covalent abortive complex between the Fpg DNA repair enzyme and DNA containing an abasic site analogue.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 683-686  [ doi:10.1107/S090744490200166X ]

Expression, purification and preliminary crystallographic studies of -amylase isozyme 1 from barley seeds

X. Robert, T. E. Gottschalk, R. Haser, B. Svensson and N. Aghajari

Synopsis: A C-terminal nonapeptide truncation improved the morphology and quality of the crystals of isozyme 1 from barley -amylase for which expression, purification and crystallization is reported

Online 22 March 2002

 

Acta Cryst. (2002). D58, 687-689  [ doi:10.1107/S0907444902001762 ]

Crystallization and preliminary X-ray diffraction analysis of fatty-acid hydroxylase cytochrome P450BS from Bacillus subtilis

D.-S. Lee, A. Yamada, I. Matsunaga, K. Ichihara, S. Adachi, S.-Y. Park and Y. Shiro

Synopsis: Crystallization and preliminary crystallographic study of cytochrome P450 from B. subtilis, which catalyzes hydroxylation of long-chain fatty acids at the and positions using H₂O₂ as an oxidant, is reported.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 690-693  [ doi:10.1107/S0907444902001890 ]

Crystallization and characterization of the dehydrogenase domain from rat peroxisomal multifunctional enzyme type 1

J. P. Taskinen, T.-R. Kiema, K. T. Koivuranta, R. K. Wierenga and J. K. Hiltunen

Synopsis: Crystals diffracting to 2.45  Å have been obtained of the enzymatically active (3S)-hydroxyacyl-CoA dehydrogenase domain of rat peroxisomal MFE-1.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 694-696  [ doi:10.1107/S0907444902002342 ]

Purification, crystallization and preliminary X-ray diffraction studies of a Ca²⁺-binding protein, human S100P

H. Zhang, Z. Wang, Y. Ding, G. Wang, X. Wang, F. Gao, H. Tang, R. Barraclough, P. S. Rudland and Z. Rao

Synopsis: Crystallization of human S100P in high protein concentration was reported. Crystals diffract to 2.0  Å and belong to space group P4₁2₁2.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 697-699  [ doi:10.1107/S0907444902002354 ]

Crystallization and preliminary X-ray diffraction analysis of two pH-dependent forms of a di-haem cytochrome c peroxidase from Pseudomonas nautica

J. M. Dias, C. Bonifácio, T. Alves, J. J. G. Moura, I. Moura and M. J. Romão

Synopsis: Cytochrome c peroxidase from P. nautica has been crystallized in two different space groups at pH 4.0 and pH 5.3  using sodium citrate and ammonium phosphate as precipitants. Data collection under cryogenic conditions allowed the characterization of the two crystal forms.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 700-703  [ doi:10.1107/S090744490200238X ]

Protein engineering for crystallization of the GTPase Sar1 that regulates ER vesicle budding

M. Huang, J. T. Weissman, C. Wang, W. E. Balch and I. A. Wilson

Synopsis: Protein engineering and dynamic light scattering provided the experimental basis to engineer a truncated form of the GTPase Sar1 that behaves well in solution and yields diffraction-quality crystals.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 704-705  [ doi:10.1107/S0907444902002676 ]

Crystallization and preliminary crystallographic analysis of a novel cytochrome P450 from Mycobacterium tuberculosis

C. G. Mowat, D. Leys, K. J. McLean, S. L. Rivers, A. Richmond, A. W. Munro, M. Ortiz Lombardia, P. M. Alzari, G. A. Reid, S. K. Chapman and M. D. Walkinshaw

Synopsis: P450 MT2 (CYP121), a novel cytochrome P450 from M. tuberculosis that binds tightly to a range of azole-based antifungal drugs, has been expressed in E. coli, purified and crystallized. The crystals belong to either space group P6₁22 or P6₅22. Native crystals diffract to 1.6  Å, while a single-site Hg-derivative crystal diffracts to 2.5  Å resolution.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 706-708  [ doi:10.1107/S0907444902002640 ]

Crystallization and preliminary X-ray analysis of the selenate reductase from Thauera selenatis

M. J. Maher and J. M. Macy

Synopsis: The selenate reductase from T. selenatis was crystallized by vapour diffusion. Diffraction data from the native and a putative heavy-atom derivative have been recorded.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 709-711  [ doi:10.1107/S0907444902003827 ]

Crystallization and preliminary X-ray characterization of a thermostable pectate lyase from Thermotoga maritima

M. A. McDonough, C. Ryttersgaard, M. E. Bjørnvad, L. Lo Leggio, M. Schülein, S. O. Schrøder Glad and S. Larsen

Synopsis: The successful crystallization and characterization by X-ray diffraction of a recombinant mutant pectate lyase from the hyperthermophilic bacterium T. maritima is described.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 712-715  [ doi:10.1107/S0907444902003001 ]

Purification and crystallization of the yeast elongation factor eEF2

R. Jørgensen, A. Carr-Schmid, P. A. Ortiz, T. G. Kinzy and G. R. Andersen

Synopsis: The protein biosynthesis elongation factor 2 from yeast has been crystallized and data collected to 2.85  Å. A yeast strain expressing the histidine-tagged factor as the only form of the protein has been constructed.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 716-718  [ doi:10.1107/S0907444902003244 ]

Purification, crystallization and preliminary X-ray diffraction of Cys103Ala acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum

C. M. H. Hensgens, E. A. Kroezinga, B. A. van Montfort, J.-M. van der Laan, J. D. Sutherland and B. W. Dijkstra

Synopsis: The C103A mutant of acyl coenzyme A:isopenicillin N, the last enzyme in penicillin G biosynthesis, was purified and crystallized. Crystals of a SeMet derivative were also obtained.

Online 22 March 2002

 

Acta Cryst. (2002). D58, 719-722  [ doi:10.1107/S0907444902001865 ]

Structural plasticity in the eight-helix fold of a trematode haemoglobin

M. Milani, A. Pesce, S. Dewilde, P. Ascenzi, L. Moens and M. Bolognesi

Synopsis: Analysis of the crystal structure of a trematode haemoglobin displaying very high O₂ affinity shows that crystal contacts in two different crystal forms markedly affect the haem-cavity stereochemistry and haem Fe coordination state.

PDB reference: 1kfr

Online 22 March 2002

 

Acta Cryst. (2002). D58, 723-726  [ doi:10.1107/S0907444902003013 ]

Crystallization and preliminary crystallographic studies of Streptococcus pyogenes cysteine protease precursor

R. Janowski, G. Bujacz, D. Gerlach and M. Jaskolski

Synopsis: Wild-type cysteine protease precursor from the human pathogen S. pyogenes was obtained in the form of crystalline flakes from which X-ray diffraction data were collected to 3.15  Å resolution at 100  K using synchrotron radiation. The crystals are monoclinic, space group P2₁, with unit-cell parameters a = 41.6, b = 136.0, c = 156.7  Å, = 95.7°, and contain four copies of the protein in the asymmetric unit.

Online 22 March 2002