Biological Crystallography

 

Acta Cryst. (2004). D60, 803-809  [ doi:10.1107/S0907444904003233 ]

An icosahedral assembly of the light-harvesting chlorophyll a/b protein complex from pea chloroplast thylakoid membranes

T. Hino, E. Kanamori, J.-R. Shen and T. Kouyama

Synopsis: The light-harvesting chlorophyll a/b protein complex (LHC-II) from pea thylakoid membranes was co-crystallized with native lipids and the resultant octahedral crystal was investigated by X-ray crystallography and cryo-electron microscopy. The crystal was shown to be made up of proteoliposomes with a diameter of 254  Å, in each of which 20 trimers of LHC-II are arranged in a T = 1 icosahedral lattice.

PDB reference: 1vcr

Online 21 April 2004

 

Acta Cryst. (2004). D60, 810-815  [ doi:10.1107/S0907444904003257 ]

Structure of the C subunit of V-type ATPase from Thermus thermophilus at 1.85  Å resolution

N. Numoto, A. Kita and K. Miki

Synopsis: The crystal structure of the C subunit of V-type H⁺-ATPase from T. thermophilus has been determined at 1.85  Å resolution. The overall structure is highly helix-rich with 20 -helices, and 3₁₀-helices and the molecule is apparently composed of three similar domains.

PDB reference: 1v9m

Online 21 April 2004

 

Acta Cryst. (2004). D60, 816-822  [ doi:10.1107/S0907444904003348 ]

Structure of C73G putidaredoxin from Pseudomonas putida

N. Smith, M. Mayhew, M. J. Holden, H. Kelly, H. Robinson, A. Heroux, V. L. Vilker and D. T. Gallagher

Synopsis: The structure of the C73G mutant of putidaredoxin (Pdx), the Fe₂S₂ ferredoxin that supplies electrons to cytochrome CYP101 (P450cam) for camphor oxidation, is reported at 1.9  Å resolution in a C2 crystal form.

PDB reference: 1r7s

Online 21 April 2004

 

Acta Cryst. (2004). D60, 823-828  [ doi:10.1107/S0907444904003907 ]

Structure of 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide bound to d(CGTACG)₂: a comparison of structures of d(CGTACG)₂ complexed with intercalators in the presence of cobalt

A. Adams, J. M. Guss, W. A. Denny and L. P. G. Wakelin

Synopsis: The structure of the complex formed between 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide and d(CGTACG)₂ has been refined to a resolution of 1.55  Å. The complex structure is very similar to six published structures of intercalators bound to d(CGTACG)₂ in the presence of cobalt. A detailed comparison of the structures is made.

PDB reference: 1rqy

NDB reference: DD0062

Online 21 April 2004

 

Acta Cryst. (2004). D60, 829-835  [ doi:10.1107/S0907444904003804 ]

Structures of two RNA octamers containing tandem G·A base pairs

S. B. Jang, K. Baeyens, M. S. Jeong, J. SantaLucia, D. Turner and S. R. Holbrook

Synopsis: The crystal structures of two RNA octamers, 5'-GGC(GA)GCC-3' and 5'-GIC(GA)GCC-3', have been determined from X-ray diffraction data to 2.8 and 2.7  Å resolution, respectively.

PDB references: 1sa9 and 1saq

Online 21 April 2004

 

Acta Cryst. (2004). D60, 836-848  [ doi:10.1107/S0907444904004123 ]

Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing

A. Teplitsky, A. Mechaly, V. Stojanoff, G. Sainz, G. Golan, H. Feinberg, R. Gilboa, V. Reiland, G. Zolotnitsky, D. Shallom, A. Thompson, Y. Shoham and G. Shoham

Synopsis: The crystal structure of the extracellular xylanase from G. stearothermophilus T-6 has been determined and refined at 2.4  Å resolution, using selenomethionyl MAD initial phases. As for other family 10 xylanases, this enzyme is made of an eightfold TIM-barrel, with two catalytic carboxylic residues in geometry typical for `retaining' glycoside hydrolases.

PDB reference: 1hiz

Online 21 April 2004

 

Acta Cryst. (2004). D60, 849-859  [ doi:10.1107/S0907444904004081 ]

The architecture of metal coordination groups in proteins

M. M. Harding

Synopsis: For 600 metal coordination groups of Ca, Mg, Mn, Fe, Cu, Zn, Na or K in a representative set of proteins from the Protein Data Bank, tables of composition and conformation are presented. For coordination groups of Ca and Zn the patterns found and the possibility of prediction are discussed.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 860-871  [ doi:10.1107/S0907444904004160 ]

Analysis of experimental time-resolved crystallographic data by singular value decomposition

S. Rajagopal, M. Schmidt, S. Anderson, H. Ihee and K. Moffat

Synopsis: Procedures for the effective application of singular value decomposition to experimental time-resolved macromolecular crystallographic data have yet to be explored systematically. In our application of singular value decomposition to a series of thirty time-resolved Laue data sets through the photocycle of the E46Q mutant of photoactive yellow protein, we develop protocols for analyzing the data in an unbiased manner and for addressing the substantial random and systematic errors present in it.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 872-877  [ doi:10.1107/S0907444904005025 ]

Crystals of the -subunit of bovine luteinizing hormone and indicators for the involvement of proteolysis in protein crystallization

A. McPherson, J. Day and L. J. Harris

Synopsis: Crystals of the -subunit of the luteinizing hormone were obtained from the intact hormone only in the presence of detergent and trypsin. The effects of proteolysis on crystallization are discussed.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 878-887  [ doi:10.1107/S0907444904004937 ]

Structure of a feruloyl esterase from Aspergillus niger

K. E. McAuley, A. Svendsen, S. A. Patkar and K. S. Wilson

Synopsis: The crystal structure of feruloyl esterase from A. niger has been determined to a resolution of 1.5  Å. In addition, the structure of feruloyl esterase complexed with its product, ferulic acid, has been obtained at 1.08  Å resolution

PDB references: 1uza and 1uwc

Online 21 April 2004

 

Acta Cryst. (2004). D60, 888-894  [ doi:10.1107/S0907444904005232 ]

A new highly integrated sample environment for protein crystallography

L. Jacquamet, J. Ohana, J. Joly, P. Legrand, R. Kahn, F. Borel, M. Pirocchi, P. Charrault, P. Carpentier and J.-L. Ferrer

Synopsis: In this paper, it is demonstrated that a new setup can be used on a synchrotron beamline to mount and centre the sample and to collect diffraction data. This new system completely changes the design of the experimental setup by merging functions that were previously considered to be distinct.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 895-902  [ doi:10.1107/S0907444904005323 ]

Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway

K. A. Kantardjieff, C.-Y. Kim, C. Naranjo, G. S. Waldo, T. Lekin, B. W. Segelke, A. Zemla, M. S. Park, T. C. Terwilliger and B. Rupp

Synopsis: The 1.7  Å native structure of the dTDP-4-keto-6-deoxyglucose epimerase encoded by the M. tuberculosis rmlC gene is reported. RmlC, the third enzyme in the M. tuberculosis dTDP-L-rhamnose pathway, is essential for mycobacterial cell-wall synthesis and is a promising target for structure-guided drug design.

PDB reference: 1upi

Online 21 April 2004

 

Acta Cryst. (2004). D60, 903-911  [ doi:10.1107/S0907444904005013 ]

Structure of OsmC from Escherichia coli: a salt-shock-induced protein

D. H. Shin, I.-G. Choi, D. Busso, J. Jancarik, H. Yokota, R. Kim and S.-H. Kim

Synopsis: The crystal structure of an osmotically inducible protein from E. coli confirmed the presence of a peroxiredoxin-like active site.

PDB reference: 1nye

Online 21 April 2004

 

Acta Cryst. (2004). D60, 912-914  [ doi:10.1107/S0907444904004536 ]

Crystallization and preliminary X-ray analysis of pseudo-merohedrally twinned crystals of the full-length ₂ subunit of the Kv1 K⁺ channel from Rattus norvegicus

T. Shimamura, O. Shamotienko, S. Akhtar, J. O. Dolly and S. Iwata

Synopsis: The full-length ₂ subunit of rat Kv1 K⁺ channel has been expressed in E. coli and crystallized. The crystals were shown to be perfectly pseudo-merohedrally twinned of the real space group P2₁2₁2 with the apparent space group P42₁2.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 915-919  [ doi:10.1107/S0907444904003762 ]

Leishmania mexicana mexicana glucose-6-phosphate isomerase: crystallization, molecular-replacement solution and inhibition

A. T. Cordeiro, R. Hardré, P. A. M. Michels, L. Salmon, L. F. Delboni and O. H. Thiemann

Synopsis: The crystallization and structural studies of two bacterially expressed L. mexicana mexicana glucose-6-phosphate isomerase (PGI) molecular constructs are presented, representing the first kinetoplastid PGI to be crystallized. One form corresponds to the natural enzyme; the second form corresponds to a form from which the N-terminal extension has been removed.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 920-922  [ doi:10.1107/S0907444904003993 ]

Expression, purification, crystallization and preliminary crystal structure analysis of the Deinococcus radiodurans organic hydroperoxide-resistance protein

C. Meunier-Jamin, U. Kapp, G. Leonard and S. McSweeney

Synopsis: The overproduction, purification and crystallization of the organic hydroperoxide-resistance protein from D. radiodurans are described. The crystals are monoclinic, space group P2₁, with unit-cell parameters a = 45.7, b = 59.6, c = 49.7  Å, = 90.43°. Preliminary X-ray diffraction data have been collected.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 923-925  [ doi:10.1107/S0907444904004263 ]

Purification, crystallization and preliminary X-ray data of the transcription factor NtcA from the cyanobacterium Anabaena PCC 7120

S. Wisén, T. Sjögren, B. Olin and B. Mannervik

Synopsis: NtcA from Anabaena PCC 7120 is a dimeric protein that consists of 223 amino acids with a molecular weight of 25  kDa per subunit. It belongs to the cAMP receptor-protein (CAP) family and is involved in the regulation of several of the genes acting in the nitrogen-fixation process. Here, the crystallization and preliminary X-ray data of NtcA are described.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 926-928  [ doi:10.1107/S0907444904004573 ]

Expression, purification and X-ray characterization of residues 18-230 from the pneumococcal histidine triad protein A (PhtA) from Streptococcus pneumoniae

A. Riboldi-Tunnicliffe, C. J. Bent, N. W. Isaacs and T. J. Mitchell

Synopsis: Crystals have been grown of the pneumococcal histidine triad protein PhtA and diffraction data collected to 1.2  Å.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 929-932  [ doi:10.1107/S090744490400472X ]

Crystallization and preliminary crystallographic analysis of BbCRASP-1, a complement regulator-acquiring surface protein of Borrelia burgdorferi

F. S. Cordes, P. Kraiczy, P. Roversi, C. Skerka, M. Kirschfink, M. M. Simon, V. Brade, E. D. Lowe, P. Zipfel, R. Wallich and S. M. Lea

Synopsis: Crystals of BbCRASP-1, a borrelial protein that binds to human factor H and factor-H-like protein-1, have been grown and diffraction data to 2.7  Å collected. Data from SeMet-labelled crystals have also been collected (to 3.2  Å): these should allow phase determination and hence structure solution.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 933-935  [ doi:10.1107/S0907444904004895 ]

Crystallization and preliminary crystallographic analysis of earthworm fibrinolytic enzyme component B from Eisenia fetida

F. Wang, C. Wang, M. Li, L. L. Gui, J. P. Zhang and W. R. Chang

Synopsis: This paper reports the crystallization and preliminary X-ray analysis of two crystal forms of earthworm fibrinolytic enzyme component B, one of which was merohedrally twinned.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 936-938  [ doi:10.1107/S0907444904005098 ]

Crystallization and preliminary X-ray diffraction analysis of three EGF domains of EMR2, a 7TM immune-system molecule

R. J. M. Abbott, V. Knott, P. Roversi, S. Neudeck, P. Lukacik, P. A. Handford and S. M. Lea

Synopsis: Three contiguous EGF modules of EMR2, an EGF-TM7 molecule, have been overexpressed, purified and crystallized. An anomalous Patterson has been calculated using data from a Ba²⁺ co-crystal and phasing is now in progress.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 939-940  [ doi:10.1107/S0907444904005190 ]

Crystallization and preliminary crystallographic analysis of a native chitinase from the fungal pathogen Aspergillus fumigatus YJ-407

H. Hu, G. Wang, H. Yang, J. Zhou, L. Mo, K. Yang, C. Jin, C. Jin and Z. Rao

Synopsis: A native chitinase from the fungal pathogen A. fumigatus YJ-407 (afCHI) has been crystallized. The crystals diffracted to 1.7  Å resolution and the structure was solved by the molecular-replacement method.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 941-944  [ doi:10.1107/S0907444904005256 ]

Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase from Pseudomonas putida

S. Alam, S. C. Wang, F. J. Ruzicka, P. A. Frey and J. E. Wedekind

Synopsis: Ornithine cyclodeaminase is a bacterial protein that converts L-ornithine into L-proline plus ammonia and is a member of the -crystallin protein family. Here, the use of high-throughput crystallization methods leading to the preparation of X-ray diffraction-quality crystals of ornithine cyclodeaminase from Pseudomonas putida is described.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 945-947  [ doi:10.1107/S0907444904006547 ]

Rhombohedral crystals of the human vinculin head domain in complex with a vinculin-binding site of talin

C. L. Rush and T. Izard

Synopsis: The crystallization and X-ray data collection to 2.4  Å of recombinant human vinculin head domain (residues 1-258) in complex with one of talin's vinculin-binding sites (residues 607-635) is reported.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 948-949  [ doi:10.1107/S0907444904005591 ]

Crystallization and preliminary X-ray crystallographic analysis of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosa

H.-L. Kim, H.-J. Yoon, J. Y. Ha, B. I. Lee, H. H. Lee, B. Mikami and S. W. Suh

Synopsis: Nicotinic acid mononucleotide adenylyltransferase from P. aeruginosa was crystallized and X-ray diffraction data were collected to 1.70  Å.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 950-951  [ doi:10.1107/S0907444904005712 ]

Crystallization and preliminary crystallographic studies of the D59A mutant of MicA, a YycF response-regulator homologue from Streptococcus pneumoniae

A. Riboldi-Tunnicliffe, M.-C. Trombe, C. J. Bent, N. W. Isaacs and T. J. Mitchell

Synopsis: A mutant of RR02, an essential response regulator from S. pneumoniae, has been crystallized and diffraction data have been collected to 1.93  Å.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 952-953  [ doi:10.1107/S0907444904006535 ]

Crystallization of the mosquito-larvicidal binary toxin produced by Bacillus sphaericus

A. W. Smith, A. Camara-Artigas and J. P. Allen

Synopsis: The binary toxin produced by B. sphaericus was crystallized using PEG 4000 and NaCl. Native data extending to a resolution of 2.7  Å have been collected.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 954-956  [ doi:10.1107/S0907444904005669 ]

Crystallization and preliminary X-ray studies of methyl parathion hydrolase from Pseudomonas sp. WBC-3

L. Sun, Y. Dong, Y. Zhou, M. Yang, C. Zhang, Z. Rao and X. Zhang

Synopsis: Methyl parathion hydrolase (MPH) from Pseudomonas sp. WBC-3, a zinc-containing enzyme that catalyzes the degradation of methyl parathion, has been purified and crystallized. A MAD data set has been collected to 2.5  Å resolution.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 957-961  [ doi:10.1107/S0907444904006158 ]

Crystallization and preliminary analysis of xenobiotic reductase A and ligand complexes from Pseudomonas putida II-B

A. M. Orville, L. Manning, D. S. Blehert, J. M. Studts, B. G. Fox and G. H. Chambliss

Synopsis: Xenobiotic reductase A catalyzes the regiospecific, NADPH dependent transformation of nitroglycerin to yield nitrite and 1,2-dinitroglycerol. This paper reports the crystallization and X-ray diffraction data analysis of the flavoenzyme.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 962-964  [ doi:10.1107/S0907444904003798 ]

Expression, purification and preliminary crystallographic studies of a single-point mutant of Mos1 mariner transposase

J. M. Richardson, L. Zhang, S. Marcos, D. J. Finnegan, M. M. Harding, P. Taylor and M. D. Walkinshaw

Synopsis: A soluble single-point mutant of Mos1 transposase has been expressed, purified and crystallized. Phase information has been obtained from a three-wavelength MAD data set collected at the selenium edge and a heavy-atom derivative.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 965-967  [ doi:10.1107/S0907444904004834 ]

Preliminary X-ray analysis of a human V_H fragment at 1.8  Å resolution

R. K. Gaur, M. B. Kupper, R. Fischer and K. M. V. Hoffmann

Synopsis: A human V_H fragment derived from the single-chain antibody scFvM12 has been crystallized and characterized at 1.8  Å resolution by X-ray diffraction.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 968-970  [ doi:10.1107/S0907444904005621 ]

Crystallization and preliminary X-ray diffraction analysis of the 16-haem cytochrome of Desulfovibrio gigas

T. Santos-Silva, J. M. Dias, G. Bourenkov, H. Bartunik, I. Moura and M. J. Romão

Synopsis: A high-molecular-weight cytochrome containing 16 c-type haems has been purified from D. gigas cells and crystallized. The crystals diffracted to beyond 2.07  Å and a MAD data set was collected.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 971-973  [ doi:10.1107/S0907444904004743 ]

Structure of the `open' form of Aspergillus nidulans 3-dehydroquinate synthase at 1.7  Å resolution from crystals grown following enzyme turnover

C. E. Nichols, A. R. Hawkins and D. K. Stammers

Synopsis: A new crystal form of the `open' conformation of A. nidulans 3-dehydroquinate synthase has been grown following addition of substrate. The structure has been solved and refined to 1.7  Å resolution.

PDB reference: 1sg6

Online 21 April 2004

 

Acta Cryst. (2004). D60, 974-977  [ doi:10.1107/S0907444904000046 ]

Purification, partial characterization, crystallization and structural determination of AHP-LAAO, a novel L-amino-acid oxidase with cell apoptosis-inducing activity from Agkistrodon halys pallas venom

H. Zhang, M. Teng, L. Niu, Y. Wang, Y. Wang, Q. Liu, Q. Huang, Q. Hao, Y. Dong and P. Liu

Synopsis: A novel L-amino-acid oxidase named AHP-LAAO with apoptosis-inducing activity was purified from A. halys pallas venom. Its crystal structure is similar to that of L-amino-acid oxidase from C. rhodostoma venom.

PDB reference: 1reo

Online 21 April 2004

 

Acta Cryst. (2004). D60, 978-982  [ doi:10.1107/S0907444904006055 ]

The pilus-retraction protein PilT: ultrastructure of the biological assembly

K. T. Forest, K. A. Satyshur, G. A. Worzalla, J. K. Hansen and T. J. Herdendorf

Synopsis: PilT pilus-retraction proteins from N. gonorrhoeae and A. aeolicus have been studied by electron microscopy and MAD-phased X-ray crystallography, respectively. A consistent picture emerges of a hexameric ring ultrastructure with a diameter of 110  Å and a height of 55  Å.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 983-984  [ doi:10.1107/S0907444904007048 ]

Untangle, a tool for filtering overlapping diffraction patterns from multicrystals

L. Buts, M.-H. Dao-Thi, L. Wyns and R. Loris

Synopsis: A simple software tool for cleaning up data from partially overlapping diffraction patterns is presented.

Online 21 April 2004

 

Acta Cryst. (2004). D60, 985-986  [ doi:10.1107/S0907444904003786 ]

Detection of L-lactate in polyethylene glycol solutions confirms the identity of the active-site ligand in a proline dehydrogenase structure

M. Zhang and J. J. Tanner

Synopsis: Some commercially available PEGs in the molecular-weight range 3000-8000 are contaminated with L-lactate. This result helps to explain the discovery of L-lactate bound in the active site of the E. coli PutA proline dehydrogenase domain crystal structure.

Online 21 April 2004