A new rotation function for molecular replacement by using both the self and cross Patterson vectors

2008 ◽  
Vol 64 (5) ◽  
pp. 561-566 ◽  
Author(s):  
Fan Jiang
Keyword(s):  
The Self ◽  
Molecular Replacement ◽  
Rotation Function

scholarly journals Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure

2021 ◽  
Vol 77 (1) ◽  
pp. 11-18
Author(s):  
Montserrat Fàbrega-Ferrer ◽  
Ana Cuervo ◽  
Francisco J. Fernández ◽  
Cristina Machón ◽  
Rosa Pérez-Luque ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Large Crystal ◽  
Rotation Matrices ◽  
Cryo Electron Microscopy ◽  
Partial Models ◽  
Medium Resolution ◽  
Experimental Phasing ◽  
Crystallographic Structures ◽  
Direct Use ◽  
Rotation Function

Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.

CRYSTALLOGRAPHIC INVESTIGATION OF ANTITHROMBIN III.

1987 ◽  
Author(s):  
J P Samama ◽  
M Delarue ◽  
D Moras ◽  
M Petitou ◽  
J C Lormeau ◽  
...  
Keyword(s):  
Technical Assistance ◽  
Antithrombin Iii ◽  
The Self ◽  
Fold Axis ◽  
Asymmetric Unit ◽  
Primary Sequence ◽  
Protein Inhibitor ◽  
Native Form ◽  
Data Set ◽  
Rotation Function

The plasma protein inhibitor anti thrombin III in its native form has been crystallized using standard techniques.The crystals diffract to about and belong to space group P41212 with cell parameters:a = b = 90.6<, c = 380.7<.The asymmetric unit contains three molecules of anti thrombin III.The self rotation function computed with the native data set indicates the presence of a non crystallographic three fold axis. Cross rotation function calculations using themodel of the cleaved α1,-antitrypsin (H. Loebermann at.,J. Mol. Biol.(1985) 177, 531) suggests tertiary structuresimilarities between the two plasma proteins.This is in agreement with the already described primary sequence homology of these glycoproteins but at variance with the model of active α1-anti trypsin inferred from the previous studies on the cleaved molecule.The technical assistance of M. Maman is deeply appreciated.

scholarly journals Expression, purification, crystallization and crystallographic study of theAspergillus terreusaromatic prenyltransferase AtaPT

2015 ◽  
Vol 71 (7) ◽  
pp. 889-894 ◽  
Author(s):  
Bingquan Gao ◽  
Ridao Chen ◽  
Xiao Liu ◽  
Jungui Dai ◽  
Fei Sun
Keyword(s):  
Aromatic Compounds ◽  
Aspergillus Terreus ◽  
Biological Properties ◽  
Chemical Diversity ◽  
The Self ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Rotation Function

Prenylated aromatics are produced by aromatic prenyltransferases during the secondary metabolism of bacteria, fungi and plants. The prenylation of nonprenylated precursors can lead to great chemical diversity and extensive biological properties.Aspergillus terreusaromatic prenyltransferase (AtaPT), which has recently been discovered and characterized, is such an enzyme and is responsible for the prenylation of various aromatic compounds. Here, recombinant AtaPT was overexpressed inEscherichia coli, purified and crystallized. Diffraction data were collected to a resolution of 1.71 Å and the crystal belonged to space groupP21212, with unit-cell parametersa= 96.2,b = 135.8,c= 69.5 Å, α = β = γ = 90°. Analysis of the calculated Matthews coefficient and the self-rotation function suggested that there are two AtaPT molecules in the asymmetric unit.

scholarly journals Using Phaser and ensembles to improve the performance of SIMBAD

2020 ◽  
Vol 76 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Adam J. Simpkin ◽  
Felix Simkovic ◽  
Jens M. H. Thomas ◽  
Martin Savko ◽  
Andrey Lebedev ◽  
...  
Keyword(s):  
Model Identification ◽  
Structural Similarity ◽  
Test Cases ◽  
Target Sequence ◽  
Molecular Replacement ◽  
Search Models ◽  
Termination Criteria ◽  
Alternative Approach ◽  
The Relationship ◽  
Rotation Function

The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.

Crystallization and preliminary X-ray diffraction of Trypanosoma cruzi dUTPase

1999 ◽  
Vol 55 (2) ◽  
pp. 528-530 ◽  
Author(s):  
V. Bernier-Villamor ◽  
A. Camacho ◽  
D. González-Pacanowska ◽  
E. Cedergren-Zeppezauer ◽  
A. Antson ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Unit Cell ◽  
The Self ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Solvent Content ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Rotation Function

Crystals of Trypanosoma cruzi dUTPase have been grown. Two different morphologies are observed, depending on the molecular weight of the PEG used as precipitating agent in the mother liquor, both having a hexagonal unit cell with similar dimensions. Complete X-ray diffraction data have been collected to low resolution for one of the forms. The space group is P6322, with unit-cell dimensions a = 134.15, c = 147.05 Å. Peaks in the self-rotation function and the solvent content are consistent with two molecules of dUTPase per asymmetric unit.

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.

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.

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