Biological Crystallography

 

Acta Cryst. (2003). D59, 203-213  [ doi:10.1107/S0907444902021479 ]

Lysosomal cysteine proteases (cathepsins): promising drug targets

D. Turk and G. Guncar

Synopsis: The physiological roles of lysosomal cysteine proteases now emerging from research are bringing them increasingly into focus as drug targets. A survey of the available crystal structures and a summary of their specificity determinants are presented here and some directions in inhibitor design are described.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 214-224  [ doi:10.1107/S0907444902018930 ]

Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model bias

J. F. Hunt and J. Deisenhofer

Synopsis: The procedures used to solve the crystal structure of the SecA translocation ATPase are described. MIR phases to a limiting resolution of 4.4 Å were extended to the 2.7 Å resolution limit of the crystals using an iterative density modification and partial model building procedure that employed real-space cross-validation to minimize model bias.

PDB references: 1m6n and 1m74

Online 24 January 2003

 

Acta Cryst. (2003). D59, 225-238  [ doi:10.1107/S0907444902018954 ]

Structural characterization of an MJ1267 ATP-binding cassette crystal with a complex pattern of twinning caused by promiscuous fiber packing

Y.-R. Yuan, O. Martsinkevich and J. F. Hunt

Synopsis: A forensic analysis is presented of a trigonal crystal form with a complex pattern of twinning including merohedral twinning of the dominant lattice. The analysis indicates that twinning is caused by promiscuous parallel and antiparallel packing of helical protein fibers, permitted by the conformational flexibility of the protein combined with the inherent plasticity of the intermolecular interactions between the fibers.

PDB reference: 1g9x

Online 24 January 2003

 

Acta Cryst. (2003). D59, 239-246  [ doi:10.1107/S0907444902020772 ]

Membrane-protein crystallization in cubo: temperature-dependent phase behaviour of monoolein-detergent mixtures

C. Sennoga, A. Heron, J. M. Seddon, R. H. Templer and B. Hankamer

Synopsis: High-quality three-dimensional crystals of membrane proteins can be produced using lipidic cubic phases. The detailed temperature-dependent phase behaviour of a wide range of monoolein-detergent mixtures is presented to aid the development of streamlined membrane-protein crystallization in cubo.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 247-254  [ doi:10.1107/S0907444902020887 ]

Structure of a hybrid squash inhibitor in complex with porcine pancreatic elastase at 1.8 Å resolution

J. Aÿ, K. Hilpert, N. Krauss, J. Schneider-Mergener and W. Höhne

Synopsis: The crystal structure of a hybrid squash-type inhibitor in complex with porcine pancreatic elastase is described. The binding loop derived from the turkey ovomucoid inhibitor third domain adopts a `canonical' conformation upon elastase binding.

PDB reference: 1mcv

Online 24 January 2003

 

Acta Cryst. (2003). D59, 255-262  [ doi:10.1107/S0907444902021467 ]

The structure of the D49 phospholipase A₂ piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possible relationship to cooperative substrate binding

D. J. Rigden, L. W. Hwa, S. Marangoni, M. H. Toyama and I. Polikarpov

Synopsis: The crystal structure of piratoxin III may represent the T-state of this phospholipase A₂ which, unusually, exhibits cooperative substrate binding.

PDB reference: 1gmz

Online 24 January 2003

 

Acta Cryst. (2003). D59, 263-273  [ doi:10.1107/S0907444902021455 ]

Actin-DBP: the perfect structural fit?

C. Verboven, I. Bogaerts, E. Waelkens, A. Rabijns, H. Van Baelen, R. Bouillon and C. De Ranter

Synopsis: The crystal structure of the actin-DBP complex was determined at 2.4 Å resolution. The implications for the actin-sequestering role of DBP and the model of the actin-filament structure are discussed.

PDB reference: 1ma9

Online 24 January 2003

 

Acta Cryst. (2003). D59, 274-289  [ doi:10.1107/S0907444902021431 ]

An automatic method to generate force-field parameters for hetero-compounds

K. Nilsson, D. Lecerof, E. Sigfridsson and U. Ryde

Synopsis: A method has been developed that automatically constructs a crystallographic refinement force field (topology and parameter files) for any molecule from a theoretical frequency calculation. The approach has been tested on five proteins containing metal sites or non-standard inhibitors or coenzymes and it is shown that the structures are improved in various aspects.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 290-298  [ doi:10.1107/S0907444902021704 ]

Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1

M. G. Rudolph, M. S. Kelker, T. R. Schneider, T. O. Yeates, V. Oseroff, D. K. Heidary, P. A. Jennings and I. A. Wilson

Synopsis: The crystal structure of a double mutant (F42W/W120F) of interleukin-1 was determined by MAD using data from merohedrally twinned crystals. The detection and overcoming of twinning in interleukin-1 crystals and an analysis of the effect of the twinning on phasing by MAD is presented.

PDB reference: 1l2h

Online 24 January 2003

 

Acta Cryst. (2003). D59, 299-303  [ doi:10.1107/S090744490202190X ]

Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6-dihydropurine riboside

T. Kinoshita, N. Nishio, I. Nakanishi, A. Sato and T. Fujii

Synopsis: The crystal structure of adenosine deaminase (ADA) from bovine intestine complexed with a transition-state analogue, 6-hydroxy-1,6-dihydropurine riboside (HDPR), was solved at 2.5 Å resolution. HDPR tightly interacts with ADA by means of six hydrogen bonds and is entirely enclosed within the active site.

PDB reference: 1krm

Online 24 January 2003

 

Acta Cryst. (2003). D59, 304-314  [ doi:10.1107/S0907444902021935 ]

SOMoRe: a multi-dimensional search and optimization approach to molecular replacement

D. C. Jamrog, Y. Zhang and G. N. Phillips

Synopsis: A new molecular-replacement code is introduced that balances local and global optimization through a global six-dimensional search of a low-resolution target function which is followed by multi-start local optimization.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 315-322  [ doi:10.1107/S0907444902022138 ]

Faster data-collection strategies for structure determination using anomalous dispersion

A. González

Synopsis: This paper discusses the results of an analysis of several data sets to determine the minimum amount of data needed to phase with SAD and MAD and the implications for the design of data-collection strategies seeking to minimize the total exposure time and dose absorbed by the crystal.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 323-333  [ doi:10.1107/S0907444902015706 ]

Refined structure of bovine carboxypeptidase A at 1.25 Å resolution

A. Kilshtain-Vardi, M. Glick, H. M. Greenblatt, A. Goldblum and G. Shoham

Synopsis: The crystal structure of bovine carboxypeptidase A has been refined at 1.25 Å resolution and allowed, together with theoretical simulations, an improved description of conformational disorder, solvent networks and protonation states in the resting enzyme.

PDB reference: 1m4l

Online 24 January 2003

 

Acta Cryst. (2003). D59, 334-337  [ doi:10.1107/S090744490201661X ]

Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana perezi

E. Valencia, A. Rosell, C. Larroy, J. Farrés, J. A. Biosca, I. Fita, X. Parés and W. F. Ochoa

Synopsis: Different crystal forms diffracting to high resolution have been obtained for two NADP(H)-dependent alcohol dehydrogenases: ScADHVI from S. cerevisiae and ADH8 from R. perezi.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 338-340  [ doi:10.1107/S0907444902017900 ]

Crystallization and preliminary X-ray diffraction analysis of O-acetylserine sulfhydrylase from Aeropyrum pernix K1

K. Mino, Y. Oda, M. Ataka and K. Ishikawa

Synopsis: An enzyme involved in cysteine biosynthesis in a hyperthermophilic archaeon has been crystallized. The crystal structure to be determined is expected to elucidate versatile substrate specificity in an ancestral-type enzyme.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 341-342  [ doi:10.1107/S0907444902020541 ]

Crystallization and preliminary X-ray analysis of a thermostable pectate lyase PL 47 from Bacillus sp. TS 47

T. Nakaniwa, T. Tada, K. Ishii, M. Takao, T. Sakai and K. Nishimura

Synopsis: The thermostable pectate lyase PL 47 from Bacillus sp. TS 47 was crystallized. A complete diffraction data set was collected to 1.8 Å resolution using synchrotron radiation.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 343-344  [ doi:10.1107/S0907444902020498 ]

Crystallization and preliminary X-ray analysis of recombinant human acid -glucocerebrosidase, a treatment for Gaucher's disease

D. Roeber, A. Achari, P. Manavalan, T. Edmunds and D. L. Scott

Synopsis: Enzyme replacement therapy is clinically effective in reducing the morbidity associated with Gaucher's disease (a lysosomal storage disorder). A 2.7 Å data set has been collected from crystals of the responsible enzyme (-glucocerebrosidase).

Online 24 January 2003

 

Acta Cryst. (2003). D59, 345-347  [ doi:10.1107/S0907444902020760 ]

Crystallization and preliminary X-ray diffraction analysis of the di-haem cytochrome c peroxidase from Pseudomonas stutzeri

C. Bonifácio, C. A. Cunha, A. Müller, C. G. Timóteo, J. M. Dias, I. Moura and M. J. Romão

Synopsis: Cytochrome c peroxidase from P. stutzeri has been crystallized using sodium citrate and PEG 8000 as precipitants. The crystals belong to space group P2₁, with unit-cell parameters a = 69.29, b = 143.31, c = 76.83 Å, = 100.78°.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 348-349  [ doi:10.1107/S0907444902020796 ]

Crystallization and preliminary X-ray diffraction studies of -cyclodextrin glucanotransferase isolated from Bacillus macerans

H.-W. Choe, K. S. Park, J. Labahn, J. Granzin, C.-J. Kim and G. Büldt

Synopsis: The -cyclodextrin glucanotransferase from B. macerans was purified homogeneously and crystallized. The crystals were suitable for X-ray analysis and diffracted to at least 2 Å.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 350-352  [ doi:10.1107/S0907444902020784 ]

Preliminary X-ray characterization of the ribonuclease P (C5 protein) from Escherichia coli: expression, crystallization and cryoconditions

H.-W. Choe, D.-G. Jeong, J. H. Park, R. Schlesinger, J. Labahn, K. P. Hofmann and G. Büldt

Synopsis: The gene for E. coli ribonuclease P protein (also known as C5 protein) and its mutant C5-C113A have been expressed as GST-fusion proteins in E. coli at a high level. After cleavage of the fusion protein, highly purified functional C5 protein is obtained that can be crystallized and characterized by X-ray diffraction.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 353-355  [ doi:10.1107/S0907444902020735 ]

Crystallization and preliminary X-ray diffraction studies of an -methylacyl-CoA racemase from Mycobacterium tuberculosis

P. Bhaumik, P. Kursula, V. Ratas, E. Conzelmann, J. K. Hiltunen, W. Schmitz and R. K. Wierenga

Synopsis: -Methylacyl-CoA racemase from M. tuberculosis has been expressed in E. coli, purified and crystallized. Native crystals belonging to space group P6₁22 or P6₅22 diffract to 2.8 Å.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 356-358  [ doi:10.1107/S0907444902020802 ]

Expression, purification and preliminary X-ray characterization of N-acetyl--glutamyl-phosphate reductase from Thermus thermophilus HB8

M. Goto, Y. Agari, R. Omi, I. Miyahara and K. Hirotsu

Synopsis: N-Acetyl--glutamyl-phosphate reductase from T. thermophilus HB8 has been expressed in E. coli, purified and crystallized. The crystals belong to space group P6₂22 or P6₄22 and diffraction data have been collected to 2.2 Å resolution.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 359-362  [ doi:10.1107/S0907444902021054 ]

Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the F1 antigen Caf1M-Caf1 chaperone-subunit pre-assembly complex from Yersinia pestis

A. Zavialov, J. Berglund and S. D. Knight

Synopsis: Crystals of the Y. pestis capsular antigen pre-assembly complex Caf1M-Caf1 have been obtained. Diffraction data from native, SeMet and Pt-labelled crystals were used to obtain a 2 Å electron-density map.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 363-365  [ doi:10.1107/S0907444902021121 ]

Crystallization and preliminary X-ray crystallographic analysis of Sclerotium rolfsii lectin

D. D. Leonidas, B. M. Swamy, A. G. Bhat, S. R. Inamdar, M. N. Kosmopoulou, E. D. Chrysina and N. G. Oikonomakos

Synopsis: The S. rolfsii lectin was crystallized and X-ray diffraction data were collected to 1.1 Å resolution.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 366-368  [ doi:10.1107/S0907444902021406 ]

Definition of domain boundaries and crystallization of the SMN Tudor domain

R. Sprangers, P. Selenko, M. Sattler, I. Sinning and M. R. Groves

Synopsis: The boundaries of the Tudor domain of the spinal muscular neuron protein SMN have been defined using NMR and crystals that diffract to 1.8 Å resolution are reported.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 369-371  [ doi:10.1107/S0907444902021418 ]

Purification, crystallization and preliminary X-ray analysis of a -like calpain

G. P. Pal, T. DeVeyra, J. S. Elce and Z. Jia

Synopsis: A hybrid calpain containing 85% of -calpain sequence, and very close in properties to -calpain, has been crystallized. The structure may help in understanding the difference in Ca²⁺ requirement between - and m-calpain.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 372-374  [ doi:10.1107/S090744490202142X ]

Crystallization and preliminary X-ray analysis of TBP-interacting protein from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1

T. Yamamoto, T. Matsuda, N. Sakamoto, H. Matsumura, T. Inoue, M. Morikawa, S. Kanaya and Y. Kai

Synopsis: The 26 kDa TBP-interacting protein from the hyperthermophilic archaeon T. kodakaraensis KOD1 (Tk-TIP26) was crystallized and the crystals diffracted to 2.2 Å. Selenomethionine-substituted Tk-TIP26 was also crystallized and MAD data was collected. A Bijvoet difference Patterson map showed strong peaks sufficient to determine the positions of the Se atoms.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 375-377  [ doi:10.1107/S0907444902072001 ]

Expression, crystallization and activities of the two family 11 aldo-keto reductases from Bacillus subtilis

A. Ehrensberger and D. K. Wilson

Synopsis: Two aldo-keto reductases from B. subtilis have been crystallized and their NADPH-dependent oxidoreductase activities have been kinetically characterized.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 378-380  [ doi:10.1107/S0907444902022175 ]

X-ray crystallographic characterization and phasing of a fucose-specific lectin from Aleuria aurantia

M. Fujihashi, D. H. Peapus, E. Nakajima, T. Yamada, J. Saito, A. Kita, Y. Higuchi, Y. Sugawara, A. Ando, N. Kamiya, Y. Nagata and K. Miki

Synopsis: A fucose-specific lectin from A. aurantia was crystallized. 2.2 Å resolution data sets were collected and phased by the MAD method using an Hg derivative.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 381-384  [ doi:10.1107/S0907444902021972 ]

Crystallization of hamster dihydroorotase: involvement of a disulfide-linked tetrameric form

M. J. Maher, D. T. C. Huang, J. M. Guss, C. A. Collyer and R. I. Christopherson

Synopsis: The dihydroorotase domain from hamster was crystallized by vapour diffusion. The crystals were found to exclusively consist of a disulfide-linked tetrameric form of the enzyme.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 385-388  [ doi:10.1107/S0907444902020310 ]

Improved three-dimensional growth of manganese superoxide dismutase crystals on the International Space Station

A. Vahedi-Faridi, J. Porta and G. E. O. Borgstahl

Synopsis: Preliminary results on the improved crystallization of manganese superoxide dismutase in the microgravity environment of the International Space Station are reported. Crystal volume was 80-times larger than the best earth crystal and diffraction to 1.26 Å resolution was observed.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 389-392  [ doi:10.1107/S0907444902020826 ]

Structure of the Yersinia enterocolitica molecular-chaperone protein SycE

C. B. Trame and D. B. McKay

Synopsis: A crystal structure of the Y. enterocolitica molecular-chaperone protein SycE shows binding of its carboxy-terminal peptide to a hydrophobic patch on a neighboring molecule.

PDB reference: 1n5b

Online 24 January 2003

 

Acta Cryst. (2003). D59, 393-395  [ doi:10.1107/S0907444902020917 ]

In-house phase determination of the lima bean trypsin inhibitor: a low-resolution sulfur-SAD case

J. É. Debreczeni, G. Bunkóczi, B. Girmann and G. M. Sheldrick

Synopsis: The unknown structure of the lima bean trypsin inhibitor was solved from the anomalous signal of the native sulfur using 3 Å in-house Cu K data and refined against 2 Å synchrotron data.

PDB reference: 1h34

Online 24 January 2003

 

Acta Cryst. (2003). D59, 396-399  [ doi:10.1107/S0907444902022011 ]

The advantages of using a modified microbatch method for rapid screening of protein crystallization conditions

A. D'Arcy, A. Mac Sweeney, M. Stihle and A. Haber

Synopsis: A modified microbatch technique is described which can be used to rapidly screen crystallization conditions. The characteristics of crystallization using silicone or paraffin oil are described.

Online 24 January 2003

 

Acta Cryst. (2003). D59, 400-403  [ doi:10.1107/S0907444902021923 ]

De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin

Y. Papanikolau, G. Tavlas, C. E. Vorgias and K. Petratos

Synopsis: Homogeneous sample of chitinase A from Serratia marcescens yielded crystals that provided a structure to 1.55 Å resolution. Co-crystallization of the enzyme with its potent inhibitor allosamidin provided the structure of the complex to 1.9 Å resolution

PDB references: 1edq and 1ffq

Online 24 January 2003

 

Acta Cryst. (2003). D59, 404  [ doi:10.1107/S0907444903000490 ]

Pushing the boundaries of molecular replacement with maximum likelihood. Erratum

R. J. Read

Synopsis: An erratum to the paper by Read (2001) Acta Cryst. D57, 1373-1382.

Online 24 January 2003