Molecular replacement with multiple different models

2004 ◽  
Vol 37 (1) ◽  
pp. 159-161 ◽  
Author(s):  
Nicholas M. Glykos ◽  
Michael Kokkinidis
Keyword(s):  
Crystal Structure ◽  
Original Description ◽  
Natural Generalization ◽  
Divide And Conquer ◽  
Search Model ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Different Types ◽  
Replacement Problem ◽  
Special Case

Classical molecular replacement methods and the newer six-dimensional searches treat molecular replacement as a succession of sub-problems of reduced dimensionality. Due to their `divide-and-conquer' approach, these methods necessarily ignore (at least during their early stages) the very knowledge that a target crystal structure may comprise, for example, more than one copy of a search model, or several models of different types. An algorithm for a stochastic multi-dimensional molecular replacement search has been described previously and shown to locate solutions successfully, even in cases as complex as a 23-dimensional 4-body search. The original description of the method only dealt with a special case of molecular replacement, namely with the problem of placingncopies of only one search model in the asymmetric unit of a target crystal structure. Here a natural generalization of this algorithm is presented to deal with the full molecular replacement problem, that is, with the problem of determining the orientations and positions of a total ofncopies ofmdifferent models (withn≥m) which are assumed to be present in the asymmetric unit of a target crystal structure. The generality of this approach is illustrated through its successful application to a 17-dimensional 3-model problem involving one DNA and two protein molecules.

The structure of plastocyanin from the cyanobacterium Phormidium laminosum

1999 ◽  
Vol 55 (2) ◽  
pp. 414-421 ◽  
Author(s):  
Charles S. Bond ◽  
Derek S. Bendall ◽  
Hans C. Freeman ◽  
J. Mitchell Guss ◽  
Christopher J. Howe ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Search Model ◽  
Molecular Replacement ◽  
Amino Acid Residues ◽  
Asymmetric Unit ◽  
Threefold Axis ◽  
Phormidium Laminosum ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The crystal structure of the `blue' copper protein plastocyanin from the cyanobacterium Phormidium laminosum has been solved and refined using 2.8 Å X-ray data. P. laminosum plastocyanin crystallizes in space group P43212 with unit-cell dimensions a = 86.57, c = 91.47 Å and with three protein molecules per asymmetric unit. The final residual R is 19.9%. The structure was solved using molecular replacement with a search model based on the crystal structure of a close homologue, Anabaena variabilis plastocyanin (66% sequence identity). The molecule of P. laminosum plastocyanin has 105 amino-acid residues. The single Cu atom is coordinated by the same residues – two histidines, a cysteine and a methionine – as in other plastocyanins. In the crystal structure, the three molecules of the asymmetric unit are related by a non-crystallographic threefold axis. A Zn atom lies between each pair of neighbouring molecules in this ensemble, being coordinated by a surface histidine residue of one molecule and by two aspartates of the other.

scholarly journals X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC

2017 ◽  
Vol 73 (1) ◽  
pp. 24-28 ◽  
Author(s):  
Matthew Wilding ◽  
Colin Scott ◽  
Thomas S. Peat ◽  
Janet Newman
Keyword(s):  
Crystal Structure ◽  
Search Model ◽  
Molecular Replacement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Acetyl Coa ◽  
Space Group ◽  
X Ray ◽  
Semialdehyde Dehydrogenase

The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 fromPseudomonassp. strain AAC makes up half of a bicistronic operon responsible for β-alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space groupP212121and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model.

scholarly journals Expression, purification and crystallization of MnSOD fromArabidopsis thaliana

2014 ◽  
Vol 70 (5) ◽  
pp. 669-672 ◽  
Author(s):  
Alexandra T. Marques ◽  
Sandra P. Santos ◽  
Margarida G. Rosa ◽  
Mafalda A. A. Rodrigues ◽  
Isabel A. Abreu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Superoxide Dismutase ◽  
Manganese Superoxide Dismutase ◽  
Search Model ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Plant Tolerance ◽  
Data Set ◽  
Manganese Superoxide ◽  
Primary Antioxidant

Manganese superoxide dismutase (MnSOD) is an essential primary antioxidant enzyme. MnSOD plays an important role in plant tolerance to abiotic stress and is a target candidate for increasing stress tolerance in crop plants. Although the structure and kinetic parameters of MnSODs from several organisms have been determined, this information is still lacking for plant MnSODs. Here, recombinant MnSOD fromArabidopsis thaliana(AtMnSOD) was expressed, purified and crystallized. A nearly complete data set could only be obtained when a total rotation range of 180° was imposed during data collection, despite the seemingly tetragonal metric of the AtMnSOD crystal diffraction. The data set extended to 1.95 Å resolution and the crystal belonged to space groupP1. Molecular-replacement calculations using an ensemble of homologous SOD structures as a search model gave a unique and unambiguous solution corresponding to eight molecules in the asymmetric unit. Structural and kinetic analysis of AtMnSOD is currently being undertaken.

scholarly journals Crystal structure of a recombinant αEC domain from human fibrinogen-420

1998 ◽  
Vol 95 (16) ◽  
pp. 9099-9104 ◽  
Author(s):  
Glen Spraggon ◽  
Dianne Applegate ◽  
Stephen J. Everse ◽  
Jian-Zhong Zhang ◽  
Leela Veerapandian ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Parent Body ◽  
Terminal Segment ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Human Fibrinogen ◽  
X Ray ◽  
Amino Terminal ◽  
Binding Cleft ◽  
Carbohydrate Ligand

The crystal structure of a recombinant αEC domain from human fibrinogen-420 has been determined at a resolution of 2.1 Å. The protein, which corresponds to the carboxyl domain of the αEchain, was expressed in and purified fromPichia pastoriscells. Felicitously, during crystallization an amino-terminal segment was removed, apparently by a contaminating protease, allowing the 201-residue remaining parent body to crystallize. An x-ray structure was determined by molecular replacement. The electron density was clearly defined, partly as a result of averaging made possible by there being eight molecules in the asymmetric unit related by noncrystallographic symmetry (P1 space group). Virtually all of an asparagine-linked sugar cluster is present. Comparison with structures of the β- and γ-chain carboxyl domains of human fibrinogen revealed that the binding cleft is essentially neutral and should not bind Gly-Pro-Arg or Gly-His-Arg peptides of the sort bound by those other domains. Nonetheless, the cleft is clearly evident, and the possibility of binding a carbohydrate ligand like sialic acid has been considered.

scholarly journals Solution of the structure of tetrameric human glucose 6-phosphate dehydrogenase by molecular replacement

1999 ◽  
Vol 55 (4) ◽  
pp. 826-834 ◽  
Author(s):  
Shannon W. N. Au ◽  
Claire E. Naylor ◽  
Sheila Gover ◽  
Lucy Vandeputte-Rutten ◽  
Deborah A. Scopes ◽  
...  
Keyword(s):  
Crystal Form ◽  
Search Model ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Data Set ◽  
Space Groups ◽  
Successful Search ◽  
Using Data ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Resolution Data

Recombinant human glucose 6-phosphate dehydrogenase (G6PD) has been crystallized and its structure solved by molecular replacement. Crystals of the natural mutant R459L grow under similar conditions in space groups P212121 and C2221 with eight or four 515-residue molecules in the asymmetric unit, respectively. A non-crystallographic 222 tetramer was found in the C2221 crystal form using a 4 Å resolution data set and a dimer of the large β + α domains of the Leuconostoc mesenteroides enzyme as a search model. This tetramer was the only successful search model for the P212121 crystal form using data to 3 Å. Crystals of the deletion mutant ΔG6PD grow in space group F222 with a monomer in the asymmetric unit; 2.5 Å resolution data have been collected. Comparison of the packing of tetramers in the three space groups suggests that the N-terminal tail of the enzyme prevents crystallization with exact 222 molecular symmetry.

scholarly journals Isolation, crystallization and crystal structure determination of bovine kidney Na+,K+-ATPase

2016 ◽  
Vol 72 (4) ◽  
pp. 282-287 ◽  
Author(s):  
Jonas Lindholt Gregersen ◽  
Daniel Mattle ◽  
Natalya U. Fedosova ◽  
Poul Nissen ◽  
Linda Reinhard
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Rectal Gland ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Animal Cells ◽  
Orthorhombic Space Group ◽  
Bovine Kidney ◽  
Shark Rectal Gland

Na+,K+-ATPase is responsible for the transport of Na+and K+across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na+,K+-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na+,K+-ATPase in a high-affinity E2–BeF3−–ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space groupC2221with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3−, ouabain and Mg2+ions.

scholarly journals Crystal structure of a putrescine aminotransferase fromPseudomonassp. strain AAC

2017 ◽  
Vol 73 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Matthew Wilding ◽  
Colin Scott ◽  
Janet Newman ◽  
Thomas S. Peat
Keyword(s):  
Crystal Structure ◽  
Heterologous Expression ◽  
Search Model ◽  
Molecular Replacement ◽  
X Rays ◽  
Space Group

The putrescine aminotransferase KES24511 fromPseudomonassp. strain AAC was previously identified as an industrially relevant enzyme based on the discovery that it is able to promiscuously catalyse the transamination of 12-aminododecanoic acid. Here, the cloning, heterologous expression, purification and successful crystallization of the KES24511 protein are reported, which ultimately generated crystals adopting space groupI2. The crystals diffracted X-rays to 2.07 Å resolution and data were collected using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4a6t as the search model.

Crystal structure images of large gold clusters and growing crystals by HRTEM

1984 ◽  
Vol 42 ◽  
pp. 428-429
Author(s):  
L.R. Wallenberg ◽  
J.-O. Bovin ◽  
G. Schmid
Keyword(s):  
Crystal Structure ◽  
Nucleation And Growth ◽  
Close Packing ◽  
Gold Clusters ◽  
Molecular Weight Determination ◽  
Growth Mechanisms ◽  
Starting Point ◽  
Different Types ◽  
Nucleation And Growth Mechanisms ◽  
Points Of View

Metallic clusters are interesting from various points of view, e.g. as a mean of spreading expensive catalysts on a support, or following heterogeneous and homogeneous catalytic events. It is also possible to study nucleation and growth mechanisms for crystals with the cluster as known starting point.Gold-clusters containing 55 atoms were manufactured by reducing (C6H5)3PAuCl with B2H6 in benzene. The chemical composition was found to be Au9.2[P(C6H5)3]2Cl. Molecular-weight determination by means of an ultracentrifuge gave the formula Au55[P(C6H5)3]Cl6 A model was proposed from Mössbauer spectra by Schmid et al. with cubic close-packing of the 55 gold atoms in a cubeoctahedron as shown in Fig 1. The cluster is almost completely isolated from the surroundings by the twelve triphenylphosphane groups situated in each corner, and the chlorine atoms on the centre of the 3x3 square surfaces. This gives four groups of gold atoms, depending on the different types of surrounding.

Alkyl-chain disorder in tetraisohexylammonium bromide

2012 ◽  
Vol 68 (4) ◽  
pp. o152-o155 ◽  
Author(s):  
Malcolm A. Kelland ◽  
Amber L. Thompson
Keyword(s):  
Crystal Structure ◽  
Crystal Growth ◽  
Alkyl Chain ◽  
Growth Inhibitor ◽  
Ammonium Cation ◽  
Asymmetric Unit ◽  
Bromide Anion ◽  
Alkyl Chains ◽  
Hydrate Crystal ◽  
Structure Ii Clathrate Hydrate

Tetraisohexylammonium bromide [systematic name: tetrakis(4-methylpentyl)azanium bromide], C24H52N+·Br−, is a powerful structure II clathrate hydrate crystal-growth inhibitor. The crystal structure, in the space groupP3221, contains one ammonium cation and one bromide anion in the asymmetric unit, both on general positions. At 100 K, the ammonium cation exhibits one ordered isohexyl chain and three disordered isohexyl chains. At 250 K, all four isohexyl chains are disordered. In an effort to reduce the disorder in the alkyl chains, the crystal was thermally cycled, but the disorder remained, indicating that it is dynamic in nature.

2,4-Diamino-6-phenyl-1,3,5-triazin-1-ium nitrate: intriguing crystal structure with high Z′/Z′′ and hydrogen bond numbers and Hirshfeld surface analysis of intermolecular interactions

CrystEngComm ◽  
2021 ◽  
Author(s):  
Nicoleta Caimac ◽  
Elena Melnic ◽  
Diana Chisca ◽  
Marina S. Fonari
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Surface Analysis ◽  
Intermolecular Interactions ◽  
Title Compound ◽  
Ionic Species ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Asymmetric Unit ◽  
Space Group

The title compound crystallises in the triclinic centrosymmetric space group P1̄ with an intriguing high number of crystallographically unique binary salt-like adducts (Z′ = 8) and a total number of ionic species (Z′′ = 16) in the asymmetric unit.

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