Literature DB >> 24037245

Exploiting tertiary structure through local folds for crystallographic phasing.

Massimo Sammito1, Claudia Millán, Dayté D Rodríguez, Iñaki M de Ilarduya, Kathrin Meindl, Ivan De Marino, Giovanna Petrillo, Rubén M Buey, José M de Pereda, Kornelius Zeth, George M Sheldrick, Isabel Usón.   

Abstract

We describe an algorithm for phasing protein crystal X-ray diffraction data that identifies, retrieves, refines and exploits general tertiary structural information from small fragments available in the Protein Data Bank. The algorithm successfully phased, through unspecific molecular replacement combined with density modification, all-helical, mixed alpha-beta, and all-beta protein structures. The method is available as a software implementation: Borges.

Mesh：

Year:  2013        PMID： 24037245     DOI： 10.1038/nmeth.2644

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  15 in total

Review 1.  Patterson correlation methods: a review of molecular replacement with CNS.

Authors:  R W Grosse-Kunstleve; P D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2001-09-21

2.  Creating structure features by data mining the PDB to use as molecular-replacement models.

Authors:  T J Oldfield
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2001-09-21

3.  Transmembrane receptor chimeras to probe HAMP domain function.

Authors:  Jürgen U Linder; Joachim E Schultz
Journal:  Methods Enzymol       Date:  2010-03-01       Impact factor: 1.600

4.  Crystallographic ab initio protein structure solution below atomic resolution.

Authors:  Dayté D Rodríguez; Christian Grosse; Sebastian Himmel; César González; Iñaki M de Ilarduya; Stefan Becker; George M Sheldrick; Isabel Usón
Journal:  Nat Methods       Date:  2009-08-16       Impact factor: 28.547

5.  Crystal structure of a beta-catenin/BCL9/Tcf4 complex.

Authors:  James Sampietro; Caroline L Dahlberg; Uhn Soo Cho; Thomas R Hinds; David Kimelman; Wenqing Xu
Journal:  Mol Cell       Date:  2006-10-20       Impact factor: 17.970

6.  On the application of the minimal principle to solve unknown structures.

Authors:  R Miller; G T DeTitta; R Jones; D A Langs; C M Weeks; H A Hauptman
Journal:  Science       Date:  1993-03-05       Impact factor: 47.728

7.  Experimental phasing with SHELXC/D/E: combining chain tracing with density modification.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

8.  High-resolution structure prediction and the crystallographic phase problem.

Authors:  Bin Qian; Srivatsan Raman; Rhiju Das; Philip Bradley; Airlie J McCoy; Randy J Read; David Baker
Journal:  Nature       Date:  2007-10-14       Impact factor: 49.962

9.  A series of PDB related databases for everyday needs.

Authors:  Robbie P Joosten; Tim A H te Beek; Elmar Krieger; Maarten L Hekkelman; Rob W W Hooft; Reinhard Schneider; Chris Sander; Gert Vriend
Journal:  Nucleic Acids Res       Date:  2010-11-11       Impact factor: 16.971

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304
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  31 in total

1.  Crystal structure of the anti-CRISPR, AcrIIC4.

Authors:  Gi Eob Kim; So Yeon Lee; Hyun Ho Park
Journal:  Protein Sci       Date:  2021-10-29       Impact factor: 6.725

2.  Crystal structure of the pheromone Er-13 from the ciliate Euplotes raikovi, with implications for a protein-protein association model in pheromone/receptor interactions.

Authors:  Bill Pedrini; Aaron D Finke; May Marsh; Pierangelo Luporini; Adriana Vallesi; Claudio Alimenti
Journal:  J Struct Biol       Date:  2021-11-17       Impact factor: 3.234

3.  Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

Authors:  Ronan M Keegan; Jaclyn Bibby; Jens Thomas; Dong Xu; Yang Zhang; Olga Mayans; Martyn D Winn; Daniel J Rigden
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-01-23

4.  Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.

Authors:  Theodoros Goulas; Danuta Mizgalska; Irene Garcia-Ferrer; Tomasz Kantyka; Tibisay Guevara; Borys Szmigielski; Aneta Sroka; Claudia Millán; Isabel Usón; Florian Veillard; Barbara Potempa; Piotr Mydel; Maria Solà; Jan Potempa; F Xavier Gomis-Rüth
Journal:  Sci Rep       Date:  2015-07-01       Impact factor: 4.379

5.  Structure of a 13-fold superhelix (almost) determined from first principles.

Authors:  Guillaume A Schoch; Massimo Sammito; Claudia Millán; Isabel Usón; Markus G Rudolph
Journal:  IUCrJ       Date:  2015-01-27       Impact factor: 4.769

Review 6.  Macromolecular ab initio phasing enforcing secondary and tertiary structure.

Authors:  Claudia Millán; Massimo Sammito; Isabel Usón
Journal:  IUCrJ       Date:  2015-01-01       Impact factor: 4.769

7.  Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.

Authors:  Bjørn Panyella Pedersen; Pontus Gourdon; Xiangyu Liu; Jesper Lykkegaard Karlsen; Poul Nissen
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

8.  Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

Authors:  Felix Simkovic; Jens M H Thomas; Ronan M Keegan; Martyn D Winn; Olga Mayans; Daniel J Rigden
Journal:  IUCrJ       Date:  2016-06-15       Impact factor: 4.769

9.  Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins.

Authors:  Sofiya Fedosyuk; Gustavo Arruda Bezerra; Katharina Radakovics; Terry K Smith; Massimo Sammito; Nina Bobik; Adam Round; Lynn F Ten Eyck; Kristina Djinović-Carugo; Isabel Usón; Tim Skern
Journal:  PLoS Pathog       Date:  2016-12-14       Impact factor: 6.823

10.  Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.

Authors:  Kevin Pröpper; Kathrin Meindl; Massimo Sammito; Birger Dittrich; George M Sheldrick; Ehmke Pohl; Isabel Usón
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-05-30
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