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

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.

Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template

1998 ◽  
Vol 54 (1) ◽  
pp. 86-89 ◽  
Author(s):  
Peer R. E. Mittl ◽  
Patrick Chène ◽  
Markus G. Grütter
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Additional Information ◽  
Nmr Structures ◽  
Replacement Method ◽  
Tetramerization Domain ◽  
Structure Solution ◽  
Molecular Replacement Method

The molecular replacement method is a powerful technique for crystal structure solution but the use of NMR structures as templates often causes problems. In this work the NMR structure of the p53 tetramerization domain has been used to solve the crystal structure by molecular replacement. Since the rotation- and translation-functions were not sufficiently clear, additional information about the symmetry of the crystal and the protein complex was used to identify correct solutions. The three-dimensional structure of residues 326–356 was subsequently refined to a final R factor of 19.1% at 1.5 Å resolution.

scholarly journals Molecular replacement then and now

2013 ◽  
Vol 69 (11) ◽  
pp. 2266-2275 ◽  
Author(s):  
Giovanna Scapin
Keyword(s):  
New York ◽  
Structural Similarity ◽  
Correct Choice ◽  
Search Model ◽  
Molecular Replacement ◽  
Acta Cryst ◽  
Replacement Method ◽  
Molecular Replacement Method ◽  
Selection Of

The `phase problem' in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962),Acta Cryst.15, 24–31]. The term `molecular replacement' was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972),The Molecular Replacement Method.New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the `best' search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to ensure that their deposited structures, which are potential search probes for future systems, are of the best possible quality.

scholarly journals Crystal structure of the aromatic-amino-acid aminotransferase fromStreptococcus mutans

2019 ◽  
Vol 75 (2) ◽  
pp. 141-146
Author(s):  
Xuzhen Cong ◽  
Xiaolu Li ◽  
Shentao Li
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Streptococcus Mutans ◽  
Aromatic Amino Acid ◽  
Aromatic Amino Acids ◽  
Diffusion Method ◽  
Molecular Replacement ◽  
Replacement Method ◽  
Molecular Replacement Method ◽  
Aromatic Amino Acid Aminotransferase

Streptococcus mutans, a facultatively aerobic and Gram-positive bacterium, is the primary causative agent of dental caries and contributes to the multispecies biofilm known as dental plaque. In this study, the aromatic-amino-acid aminotransferase fromStreptococcus mutans(SmAroAT) was recombinantly expressed inEscherichia coli. An effective purification protocol was established. The recombinant protein was crystallized using the hanging-drop vapor-diffusion method with PEG 3350 as the primary precipitant. The crystal structure ofSmAroAT was solved at 2.2 Å resolution by the molecular-replacement method. Structural analysis indicated that the proteins of the aromatic-amino-acid aminotransferase family have conserved structural elements that might play a role in substrate binding. These results may help in obtaining a better understanding of the catabolism and biosynthesis of aromatic amino acids.

AUTOMR: an automatic processing program system for the molecular replacement method

1991 ◽  
Vol 24 (6) ◽  
pp. 1063-1066 ◽  
Author(s):  
Y. Matsuura
Keyword(s):  
Automatic Processing ◽  
Molecular Replacement ◽  
Initial Model ◽  
Program System ◽  
Replacement Method ◽  
Model Molecule ◽  
Translation Function ◽  
Processing Program ◽  
Molecular Replacement Method ◽  
Rotation Function

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.

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

1998 ◽  
Vol 54 (1) ◽  
pp. 90-92 ◽  
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.

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

2015 ◽  
Vol 71 (4) ◽  
pp. 466-470 ◽  
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.

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

2014 ◽  
Vol 70 (4) ◽  
pp. 535-537 ◽  
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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