Literature DB >> 19684596

Crystallographic ab initio protein structure solution below atomic resolution.

Dayté D Rodríguez1, Christian Grosse, Sebastian Himmel, César González, Iñaki M de Ilarduya, Stefan Becker, George M Sheldrick, Isabel Usón.   

Abstract

Ab initio macromolecular phasing has been so far limited to small proteins diffracting at atomic resolution (beyond 1.2 A) unless heavy atoms are present. We describe a general ab initio phasing method for 2 A data, based on combination of localizing model fragments such as small á-helices with Phaser and density modification with SHELXE. We implemented this approach in the program Arcimboldo to solve a 222-amino-acid structure at 1.95 A.

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Year:  2009        PMID： 19684596     DOI： 10.1038/nmeth.1365

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


  12 in total

1.  Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation. Elucidation of the phosphorylation chain leading to inactivation of GlcT.

Authors:  Matthias H Schmalisch; Steffi Bachem; Jörg Stülke
Journal:  J Biol Chem       Date:  2003-10-03       Impact factor: 5.157

2.  Refinement of macromolecular structures by the maximum-likelihood method.

Authors:  G N Murshudov; A A Vagin; E J Dodson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1997-05-01

3.  Phasing at resolution higher than the experimental resolution.

Authors:  Rocco Caliandro; Benedetta Carrozzini; Giovanni L Cascarano; Liberato De Caro; Carmelo Giacovazzo; Dritan Siliqi
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-04-20

4.  A modified ACORN to solve protein structures at resolutions of 1.7 A or better.

Authors:  Yao Jia-xing; M M Woolfson; K S Wilson; E J Dodson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-10-19

5.  Structure determination of the O-methyltransferase NovP using the 'free lunch algorithm' as implemented in SHELXE.

Authors:  Isabel Usón; Clare E M Stevenson; David M Lawson; George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-09-19

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.  The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.

Authors:  F X Gomis-Rüth; M Solá; P Acebo; A Párraga; A Guasch; R Eritja; A González; M Espinosa; G del Solar; M Coll
Journal:  EMBO J       Date:  1998-12-15       Impact factor: 11.598

8.  Structure of oxidized bacteriophage T4 glutaredoxin (thioredoxin). Refinement of native and mutant proteins.

Authors:  H Eklund; M Ingelman; B O Söderberg; T Uhlin; P Nordlund; M Nikkola; U Sonnerstam; T Joelson; K Petratos
Journal:  J Mol Biol       Date:  1992-11-20       Impact factor: 5.469

9.  Automated main-chain model building by template matching and iterative fragment extension.

Authors:  Thomas C Terwilliger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-12-19

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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  74 in total

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Authors:  Subramaniapillai Kolappan; Erin N Tracy; Lauren O Bakaletz; Robert S Munson; Lisa Craig
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-02-22

2.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

3.  A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography.

Authors:  Richard D Bunker; Kalyaneswar Mandal; Ghader Bashiri; Jessica J Chaston; Bradley L Pentelute; J Shaun Lott; Stephen B H Kent; Edward N Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-23       Impact factor: 11.205

4.  Exploiting tertiary structure through local folds for crystallographic phasing.

Authors:  Massimo Sammito; 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
Journal:  Nat Methods       Date:  2013-09-15       Impact factor: 28.547

5.  Ab initio solution of macromolecular crystal structures without direct methods.

Authors:  Airlie J McCoy; Robert D Oeffner; Antoni G Wrobel; Juha R M Ojala; Karl Tryggvason; Bernhard Lohkamp; Randy J Read
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-21       Impact factor: 11.205

6.  MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.

Authors:  Jouko J Virtanen; Yang Zhang
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-06-08       Impact factor: 7.652

7.  Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO.

Authors:  Jan Abendroth; Banumathi Sankaran; Peter J Myler; Donald D Lorimer; Thomas E Edwards
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2018-08-29       Impact factor: 1.056

Review 8.  Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.

Authors:  Paul D Adams; David Baker; Axel T Brunger; Rhiju Das; Frank DiMaio; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger
Journal:  Annu Rev Biophys       Date:  2013-02-28       Impact factor: 12.981

9.  High-resolution crystal structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli.

Authors:  Cecilia Artola-Recolons; César Carrasco-López; Leticia I Llarrull; Malika Kumarasiri; Elena Lastochkin; Iñaki Martínez de Ilarduya; Kathrin Meindl; Isabel Usón; Shahriar Mobashery; Juan A Hermoso
Journal:  Biochemistry       Date:  2011-03-08       Impact factor: 3.162

10.  A highly conserved region essential for NMD in the Upf2 N-terminal domain.

Authors:  Zaineb Fourati; Bijoyita Roy; Claudia Millan; Pierre-Damien Coureux; Stéphanie Kervestin; Herman van Tilbeurgh; Feng He; Isabel Usón; Allan Jacobson; Marc Graille
Journal:  J Mol Biol       Date:  2014-09-30       Impact factor: 5.469
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