Biological Crystallography

 

Acta Cryst. (2002). D58, 1-9  [ doi:10.1107/S0907444901016444 ]

Gd-HPDO3A, a complex to obtain high-phasing-power heavy-atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozyme

É. Girard, L. Chantalat, J. Vicat and R. Kahn

Synopsis: A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme were obtained by co-crystallization using different concentrations of the complex. Diffraction data from three derivative crystals were collected to a resolution of 1.7  Å using Cu  K radiation from a rotating anode.

PDB reference: 1h87

Online 21 December 2001

 

Acta Cryst. (2002). D58, 10-20  [ doi:10.1107/S0907444901016699 ]

Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase

E. Rudiño-Piñera, S. Morales-Arrieta, S. P. Rojas-Trejo and E. Horjales

Synopsis: A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed description of the heterotropic allosteric transition in which structural flexibility plays a central role.

PDB references: 1fqo, 1frz, 1fs5, 1fs6 and 1fsf

Online 21 December 2001

 

Acta Cryst. (2002). D58, 21-28  [ doi:10.1107/S0907444901016808 ]

De novo phasing of two crystal forms of tryparedoxin II using the anomalous scattering from S atoms: a combination of small signal and medium resolution reveals this to be a general tool for solving protein crystal structures

E. Micossi, W. N. Hunter and G. A. Leonard

Synopsis: The structures of two crystal forms of tryparedoxin II from C. fasciculata have been determined de novo by exploiting the anomalous scattering at 1.77  Å wavelength of the S atoms in the native protein.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 29-38  [ doi:10.1107/S0907444901017267 ]

The 2.6  Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position'

D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry

Synopsis: The first structure of a bacterioferritin from a photosynthetic organism (R. capsulatus) was solved by the MIR method at 2.6  Å resolution in the I422 space group and compared with that from E. coli solved in the P2₁ and P4₂2₁2 space groups. The new crystals reveal for the first time the presence of the non-symmetric heme molecule on a twofold crystallographic axis. It is concluded that in the crystal each heme site contains a symmetrical mixture of heme in two orientations.

PDB reference: 1jgc

Online 21 December 2001

 

Acta Cryst. (2002). D58, 39-59  [ doi:10.1107/S0907444901017279 ]

The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65  Å resolution

S. D. Benson, J. K. H. Bamford, D. H. Bamford and R. M. Burnett

Synopsis: P3 is a trimer of double viral jelly rolls and so has an architecture similar to hexon, its counterpart in the mammalian adenovirus. The X-ray structure at 1.65  Å resolution shows flexible loops at locations important for capsid interactions and an intricate water network that appears to contribute additional stability to the `trimerization loops' at the top of the molecule.

PDB references: 1hx6 and 1hqn

Online 21 December 2001

 

Acta Cryst. (2002). D58, 60-69  [ doi:10.1107/S0907444901017292 ]

Low-resolution detergent tracing in protein crystals using xenon or krypton to enhance X-ray contrast

O. Sauer, M. Roth, T. Schirmer, G. Rummel and C. Kratky

Synopsis: The use of xenon and krypton as hydrophobic probes to distinguish between aqueous and detergent solvent regions in crystals of the membrane protein OmpF porin by conventional X-ray crystallography is assessed.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 70-80  [ doi:10.1107/S0907444901017309 ]

The crystal and molecular structures of diferric porcine and rabbit serum transferrins at resolutions of 2.15 and 2.60  Å, respectively

D. R. Hall, J. M. Hadden, G. A. Leonard, S. Bailey, M. Neu, M. Winn and P. F. Lindley

Synopsis: The X-ray structures of rabbit and porcine serum transferrins are reported at resolutions of 2.6 and 2.15  Å, respectively. The more acid-labile release of iron from serum transferrins than from lactoferrins is discussed.

PDB references: 1h76 and 1jnf

Online 21 December 2001

 

Acta Cryst. (2002). D58, 81-89  [ doi:10.1107/S0907444901017383 ]

X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution

H. Shimizu, S.-Y. Park, Y. Shiro and S. Adachi

Synopsis: Crystal structures of the nitric oxide reductase cytochrome P450nor in the ferric resting and the ferrous carbonmonoxy (CO) states have been determined at 1.00 and 1.05  Å resolution, respectively.

PDB references: 1jfb and 1jfc

Online 21 December 2001

 

Acta Cryst. (2002). D58, 90-96  [ doi:10.1107/S0907444901017668 ]

Sine-enhanced Shake-and-Bake: the theoretical basis and applications to Se-atom substructures

H. Xu, H. A. Hauptman and C. M. Weeks

Synopsis: The sine-enhanced minimal function and the corresponding sine-enhanced Shake-and-Bake procedure have been proposed and tested. With proper choice of parameter values, the sine-enhanced Shate-and-Bake procedure outperformed the traditional Shake-and-Bake by a two- to eightfold increase in success rate for Se-atom substructures.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 97-103  [ doi:10.1107/S0907444901018145 ]

Generation of noble-gas binding sites for crystallographic phasing using site-directed mutagenesis

M. L. Quillin and B. W. Matthews

Synopsis: A novel approach for de novo phase determination using site-directed mutagenesis to generate noble-gas binding sites in proteins is described. MIR phases from xenon derivatives obtained using this method compare favorably with MAD phases from selenomethionine substitution.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 104-110  [ doi:10.1107/S0907444901018170 ]

Structure of an acidic phospholipase A₂ from the venom of Deinagkistrodon acutus

L. Gu, H. Zhang, S. Song, Y. Zhou and Z. Lin

Synopsis: The structure of an acidic PLA₂ from D. acutus been determined by molecular replacement with significant conformational differences observed in segment 14-23 of the two molecules in the asymmetric unit. This segment is related to the interface recognition site.

PDB reference: 1ijl

Online 21 December 2001

 

Acta Cryst. (2002). D58, 111-119  [ doi:10.1107/S0907444901018479 ]

A branched N-linked glycan at atomic resolution in the 1.12  Å structure of rhamnogalacturonan acetylesterase

A. Mølgaard and S. Larsen

Synopsis: The structure of the glycoprotein rhamnogalacturonan acetylesterase has been refined at 1.12  Å resolution. The branched N-linked glycan structure has been refined without target values for bond lengths and angles and the resulting values are compared with the current dictionary values obtained from small-molecule studies.

PDB reference: 1k7c

Online 21 December 2001

 

Acta Cryst. (2002). D58, 120-123  [ doi:10.1107/S0907444901013312 ]

Crystallization of the Z domain of the human editing enzyme ADAR1 complexed with a DNA-RNA chimeric oligonucleotide in the left-handed Z-conformation

B. A. Brown, A. Athanasiadis, E. B. Hanlon, K. Lowenhaupt, C. M. Wilbert and A. Rich

Synopsis: The Z domain of human ADAR1 has been cocrystallized with the chimeric oligonucleotide (dCrG)₃ in the Z-conformation.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 124-126  [ doi:10.1107/S0907444901019941 ]

Crystallization and preliminary X-ray crystallographic studies of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly

H. Nakano, S. Uchiyama, T. Yoshida, T. Ohkubo, H. Kato, Y. Yamagata and Y. Kobayashi

Synopsis: Ribosome recycling factor from E. coli has been crystallized in space group P2₁ with no additives. Data were collected to 2.2  Å and molecular replacement gave solutions for the rotation and translation functions.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 127-129  [ doi:10.1107/S090744490101650X ]

Crystallization and preliminary crystallographic analysis of a metastasis-inducing protein, human S100A4

H. Zhang, Z. Wang, Y. Ding, G. Wang, X. Wang, M. Bartlam, H. Tang, Y. Liu, F. Jiang, R. Barraclough, P. S. Rudland and Z. Rao

Synopsis: SeMet S100A4 (human) has been crystallized using similar conditions to those used for the native protein. SeMet S100A4 crystals diffract better than the native for data collection and belong to space group P6 or P3.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 130-132  [ doi:10.1107/S0907444901016663 ]

Crystallization and preliminary crystallographic studies of five crystal forms of Escherichia coli L-asparaginase II (Asp90Glu mutant)

M. Kozak, D. Borek, R. Janowski and M. Jaskólski

Synopsis: E. coli L-asparaginase II with a Asp90Glu mutation in the active site has been crystallized in five polymorphic forms.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 133-134  [ doi:10.1107/S0907444901017310 ]

Purification, crystallization and preliminary X-ray diffraction analysis of human phosphoserine phosphatase

Y. Peeraer, A. Rabijns, C. Verboven, J.-F. Collet, E. Van Schaftingen and C. De Ranter

Synopsis: Phosphoserine phosphatase, a human enzyme involved in the L-serine biosynthesis pathway, has been purified and crystals suitable for structural analysis have been obtained.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 135-139  [ doi:10.1107/S0907444901017346 ]

Expression, crystallization and preliminary X-ray analysis of human and rabbit 20-hydroxysteroid dehydrogenases in complex with NADP(H) and various steroid substrates

J.-F. Couture, L. Cantin, P. Legrand, V. Luu-The, F. Labrie and R. Breton

Synopsis: The human and rabbit 20-hydroxysteroid dehydrogenases, which catalyse the inactivation of progesterone, have been expressed in E. coli, purified and subsequently crystallized. Several crystal complexes have been obtained and three of them diffract to better than 2.0  Å resolution.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 140-142  [ doi:10.1107/S0907444901017437 ]

Crystallization and preliminary X-ray analysis of human nicotinamide mononucleotide adenylyltransferase (NMNAT)

E. Werner, M. Ziegler, F. Lerner, M. Schweiger, Y. A. Muller and U. Heinemann

Synopsis: The human form of nicotinamide mononucleotide adenylyltransferase which catalyses the final step in the synthesis of nicotinamide-adenine dinucleotide (NAD⁺) by transferring the adenylyl moiety of ATP to nicotinamide mononucleotide with the release of pyrophosphate has been crystallized in the presence of NAD⁺.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 143-144  [ doi:10.1107/S0907444901017358 ]

Crystallization and preliminary crystallographic study of an invertebrate C-type lectin, CEL-I, from the marine invertebrate Cucumaria echinata

T. Hatakeyama, N. Matsuo, H. Aoyagi, H. Sugawara, T. Uchida, G. Kurisu and M. Kusunoki

Synopsis: An invertebrate C-type lectin, CEL-I, from the marine invertebrate C. echinata was crystallized and 2.0  Å resolution data were collected using synchrotron radiation.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 145-147  [ doi:10.1107/S090744490101736X ]

Crystallization and preliminary crystallographic studies of dimeric disintegrins from the venom of two Agkistrodon snakes

Y. Fujii, D. Okuda, Z. Fujimoto, T. Morita and H. Mizuno

Synopsis: Two dimeric disintegrins named PVS and acostatin were crystallized and data were collected to 2.0 and 2.8  Å resolution, respectively.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 148-150  [ doi:10.1107/S0907444901017371 ]

Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37  K

T. Motoyama, M. Nakasako and I. Yamaguchi

Synopsis: Scytalone dehydratase Phe162Ala variant is a good target for investigating the substrate-binding mechanism of the enzyme. the variant enzyme was crystallized in its unligated state, and the diffraction data of the crystal were collected at 37  K using synchrotron X-rays.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 151-153  [ doi:10.1107/S0907444901017401 ]

Crystallization of a large single crystal of a B-DNA decamer for a neutron diffraction experiment by the phase-diagram technique

S. Arai, T. Chatake, Y. Minezaki and N. Niimura

Synopsis: Crystallization of a large single crystal of a B-DNA decamer, d(CCATTAATGG), for a neutron-diffraction experiment has been accomplished by an analysis of its solubility phase diagram and a large single crystal was successfully crystallized at around the minimum solubility point of the oligonucleotide.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 154-156  [ doi:10.1107/S0907444901017528 ]

Cloning, expression and preliminary X-ray analysis of the dihydroorotase from the hyperthermophilic eubacterium Aquifex aeolicus

C. Purcarea, P. Martin, J. F. Vickrey, H. I. Guy, B. F. P. Edwards and D. R. Evans

Synopsis: Dihydroorotase from the extreme hyperthermophile A. aeolicus was cloned and expressed at high levels in E. coli. Crystals of the purified wild type and selelnomethionine-substituted enzyme, space group C2, diffracted to a resolution of 1.7  Å.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 157-159  [ doi:10.1107/S0907444901017735 ]

Crystallization and preliminary X-ray diffraction studies of catalase-peroxidase from Synechococcus PCC 7942

K. Wada, T. Tada, Y. Nakamura, T. Kinoshita, M. Tamoi, S. Shigeoka and K. Nishimura

Synopsis: Catalase-peroxidase from Synechococcus PCC 7942 has been purified and crystallized in the tetragonal space group P4₁2₁2 or P4₃2₂1. A native data set has been collected to 2.3  Å resolution using the SPring-8 synchrotron-radiation source.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 160-162  [ doi:10.1107/S0907444901017723 ]

Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli

M. Jormakka, S. Törnroth, J. Abramson, B. Byrne and S. Iwata

Synopsis: A membrane-protein complex, formate dehydrogenase-N from E. coli, has been purified and crystallized.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 163-164  [ doi:10.1107/S090744490101811X ]

Crystallization and preliminary X-ray diffraction analysis of monkey dimeric dihydrodiol dehydrogenase

O. El-Kabbani, R.P.-T. Chung, P. A. Ramsland, Y. Asada, S. Ishikura, N. Usami and A. Hara

Synopsis: Hexagonal crystals of dimeric dihydrodiol dehydrogenase from monkey were grown from buffered ammonium phosphate solutions. This is the first crystallization report of a dimeric dihydrodiol dehydrogenase.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 165-166  [ doi:10.1107/S0907444901018169 ]

Crystallization and preliminary crystallographic analysis of the soluble -glycerophosphate oxidase from Streptococcus sp.

C. M. Finnerty, V. Charrier, A. Claiborne and P. A. Karplus

Synopsis: The crystallization of soluble FAD-dependent -glycerophosphate oxidase from Streptococcus sp. is reported. Synchrotron X-ray radiation was used to collect diffraction data to 2.4  Å resolution.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 167-169  [ doi:10.1107/S0907444901018236 ]

Crystallization and preliminary X-ray diffraction analysis of the seed lectin from Parkia platycephala

F. Gallego del Sol, S. Ramón-Maiques, C. F. Santos, T. B. Grangeiro, C. S. Nagano, C. M. S. A. Farias, B. S. Cavada and J. J. Calvete

Synopsis: Crystallization and preliminary X-ray diffraction analysis of P. platycephala lectin, a Mimosoideae regarded as the most primitive group of Leguminosae plants, are reported. Resolution of this structure will show the arrangement of three tandem beta-prism domains, a novel architecture for a leguminous lectin.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 170-172  [ doi:10.1107/S0907444901018248 ]

Crystallization and preliminary X-ray studies of the protease domain of the heat-shock protein HtrA from Thermotoga maritima

D. Y. Kim and K. K. Kim

Synopsis: The protease domain of T. maritima HtrA has been purified and crystallized. The crystals diffracted to 2.7  Å resolution.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 173-175  [ doi:10.1107/S0907444901018649 ]

Crystallization and preliminary X-ray crystallographic studies of a macromolecular antitumour antibiotic, C1027

Y. Chen, R. Shao, M. Bartlam, J. Li, L. Jin, Y. Gao, Y. Liu, H. Tang, Y. Zhen and Z. Rao

Synopsis: C1027 is a macromolecular antitumour antibiotic produced by Streptomyces globispourus C1027 and consists of an apoprotein and a non-protein labile chromophore. The purified C1027 was monodisperse according to dynamic light-scattering measurements and crystallized in two different crystal forms from two different starting conditions using the vapour-diffusion method.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 176-178  [ doi:10.1107/S0907444901019618 ]

Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1

R. M. de Jong, H. J. Rozeboom, K. H. Kalk, L. Tang, D. B. Janssen and B. W. Dijkstra

Synopsis: Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. The enantioselective halohydrin dehalogenase HheC from A. radiobacter AD1 was crystallized and data were collected to 3.0  Å resolution.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 179-181  [ doi:10.1107/S0907444901019874 ]

Expression, purification, crystallization and preliminary X-ray analysis of the acyl carrier protein synthase (acpS) from Mycobacterium tuberculosis

S. Chopra, S. Kumar Singh, S. Prasad Sati, A. Ranganathan and A. Sharma

Synopsis: Acyl carrier protein synthase (acpS) catalyzes the formation of holo-ACP, which mediates the transfer of acyl fatty-acid intermediates during the biosynthesis of fatty acids and lipids. The M. tuberculosis enzyme has been expressed and purified, and then crystallized by the vapour-diffusion method using 2-propanol as a precipitant.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 182-185  [ doi:10.1107/S0907444901015803 ]

Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable lipase from Bacillus stearothermophilus P1

S. Sinchaikul, J. D. A. Tyndall, L. A. Fothergill-Gilmore, P. Taylor, S. Phutrakul, S.-T. Chen and M. D. Walkinshaw

Synopsis: A thermostable lipase from B. stearothermophilus P1 has been overexpressed, purified and crystallized.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 186-187  [ doi:10.1107/S0907444901018455 ]

Crystallization and preliminary crystallographic investigation of a low-pH native insulin monomer with flexible behaviour

Y. Zhang, J. L. Whittingham, J. P. Turkenburg, E. J. Dodson, J. Brange and G. G. Dodson

Synopsis: Porcine insulin has been crystallized as a monomer in the presence of 20% acetic acid. X-ray data has been collected to 1.6  Å resolution.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 188  [ doi:10.1107/S0907444901021126 ]

The X-ray structure of a recombinant major urinary protein at 1.75  Å resolution. A comparative study of X-ray and NMR-derived structures. Addendum

P. R. Kuser, L. Franzoni, E. Ferrari, A. Spisni and I. Polikarpov

Synopsis: Addendum to Acta Cryst. (2001), D57, 1863-1869.

Online 21 December 2001

 

Acta Cryst. (2002). D58, 189-194  [ doi:10.1107/S0907444901019473 ]

Notes for authors

Online 21 December 2001