The molecular replacement method. I. The rotation function problem, application to bovine liver catalase and STNV

An automatic processing program system of the molecular replacement method AUTOMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases.

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OVIONE: a new vector-search rotation-function program for macromolecular crystallography

Journal of Applied Crystallography ◽

10.1107/s0021889800011456 ◽

2000 ◽

Vol 33 (6) ◽

pp. 1436-1444

Author(s):

Carmen Álvarez-Rúa ◽

Javier Borge ◽

Santiago García-Granda

Keyword(s):

Crystal Structure ◽

Careful Analysis ◽

Molecular Replacement ◽

Macromolecular Crystallography ◽

Minimization Algorithm ◽

Statistical Parameters ◽

Replacement Method ◽

Molecular Replacement Method ◽

Rotation Function ◽

Selection Of

A computer program (OVIONE) that uses a new vector-search rotation function for crystal-structure determination by the molecular-replacement method has been developed. Image-seeking functions have proved to be useful rotation functions in macromolecular crystallography, provided that some conditions on the statistical parameters of both the crystal and the model Patterson maps are fulfilled. An appropriate selection of the vectors involved in the calculation of the image-seeking functions is crucial for the success of the proposed procedure. This selection relies on certain parameters, a careful analysis of which has been performed in order to establish optimal ranges in which the discrimination of the rotation function is enhanced. Finally, the refinement of the highest peaks of the rotation function is carried out by making use of a simple and quick minimization algorithm.

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Crystallization and preliminary structural studies of Scilla campanulata lectin complexed with α1–6 mannobiose

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444997007063 ◽

1998 ◽

Vol 54 (1) ◽

pp. 90-92 ◽

Cited By ~ 1

Author(s):

Lisa M Wright ◽

Stephen D. Wood ◽

Colin D. Reynolds ◽

Pierre J. Rizkallah ◽

Anthony K. Allen

Keyword(s):

Molecular Replacement ◽

X Rays ◽

Synchrotron Source ◽

Replacement Method ◽

Cell Dimensions ◽

Molecular Replacement Method ◽

Hanging Drop Method ◽

Unit Cell Dimensions ◽

Antiretroviral Activity ◽

Image Plate System

Recent work has shown that Scilla campanulata agglutinin from bluebell bulbs has a strong affinity for α(1,3)- and α(1,6)-linked mannosyl residues and possesses moderate antiretroviral activity. This lectin has been crystallized by the hanging-drop method of vapour diffusion complexed with the disaccharide mannose-α1,6-D-mannose. The crystals are in the space group P21212 with unit-cell dimensions a = 70.63, b = 92.79 and c = 47.25 Å, and with a dimer in the asymmetric unit. The crystals diffract X-rays to beyond 1.5 Å resolution at 277 K and are stable in an X-ray beam. Data to 1.6 Å resolution have been collected using a MAR image-plate system at a synchrotron source and the structure of the complex has been solved by the molecular replacement method.

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Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF fromMicrocystis aeruginosa, a putative reductase participating in aeruginosin biosynthesis

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x15005063 ◽

2015 ◽

Vol 71 (4) ◽

pp. 466-470 ◽

Cited By ~ 1

Author(s):

Ruyi Ding ◽

Cui Xu ◽

Xu Chen ◽

Mengyun Bao ◽

Xiaoting Qiu

Keyword(s):

Diffraction Analysis ◽

Biosynthetic Pathway ◽

Molecular Replacement ◽

X Ray Diffraction ◽

Antithrombotic Activity ◽

X Ray ◽

Cell Parameters ◽

Maximum Resolution ◽

Replacement Method ◽

Molecular Replacement Method

The 2-carboxy-6-hydroxyoctahydroindole moiety is an essential residue for the antithrombotic activity of aeruginosins, which are a class of cyanobacteria-derived bioactive linear tetrapeptides. The biosynthetic pathway of the 2-carboxy-6-hydroxyoctahydroindole moiety has not yet been resolved. AerF was indicated to be involved in the biosynthesis of the 2-carboxy-6-hydroxyoctahydroindole moiety. This study reports the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF fromMicrocystis aeruginosawith a C-terminal His6tag. The crystal diffracted to a maximum resolution of 1.38 Å and belonged to the tetragonal space groupP4322, with unit-cell parametersa=b= 101.581,c= 116.094 Å. The calculated Matthews coefficient and solvent content of the crystal were 2.47 Å3 Da−1and 50.32%, respectively. The initial model of the structure was obtained by the molecular-replacement method and refinement of the structure is in progress.

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Crystallization and preliminary X-ray crystallographic analysis of PBPD2 fromListeria monocytogenes

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14005470 ◽

2014 ◽

Vol 70 (4) ◽

pp. 535-537 ◽

Cited By ~ 1

Author(s):

Hyung Jin Cha ◽

Jae-Hee Jeong ◽

Yeon-Gil Kim

Keyword(s):

Biosynthetic Pathway ◽

Crystallographic Analysis ◽

Diffusion Method ◽

Low Molecular Weight ◽

Molecular Replacement ◽

Orthorhombic Space Group ◽

Penicillin Binding Proteins ◽

Cell Parameters ◽

Replacement Method ◽

Molecular Replacement Method

Penicillin-binding proteins (PBPs), which mediate the peptidoglycan biosynthetic pathway in the bacterial cell wall, have been intensively investigated as a target for the design of antibiotics. In this study, PBPD2, a low-molecular-weight PBP encoded bylmo2812fromListeria monocytogenes, was overexpressed inEscherichia coli, purified and crystallized at 295 K using the sitting-drop vapour-diffusion method. The crystal belonged to the primitive orthorhombic space groupP212121, with unit-cell parametersa= 37.7,b= 74.7,c= 75.1 Å, and diffracted to 1.55 Å resolution. There was one molecule in the asymmetric unit. The preliminary structure was determined by the molecular-replacement method.

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