Literature DB >> 18034855

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.

Alexander Wlodawer1, Wladek Minor, Zbigniew Dauter, Mariusz Jaskolski.   

Abstract

The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45,000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.

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Year:  2007        PMID: 18034855      PMCID: PMC4465431          DOI: 10.1111/j.1742-4658.2007.06178.x

Source DB:  PubMed          Journal:  FEBS J        ISSN: 1742-464X            Impact factor:   5.542


  63 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.

Authors:  C Jelsch; M M Teeter; V Lamzin; V Pichon-Pesme; R H Blessing; C Lecomte
Journal:  Proc Natl Acad Sci U S A       Date:  2000-03-28       Impact factor: 11.205

3.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

Authors:  N Ban; P Nissen; J Hansen; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

4.  Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide.

Authors:  B Rupp; B Segelke
Journal:  Nat Struct Biol       Date:  2001-08

5.  The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.

Authors:  Istvan Botos; Edward E Melnikov; Scott Cherry; Joseph E Tropea; Anna G Khalatova; Fatima Rasulova; Zbigniew Dauter; Michael R Maurizi; Tatyana V Rotanova; Alexander Wlodawer; Alla Gustchina
Journal:  J Biol Chem       Date:  2003-12-09       Impact factor: 5.157

6.  Triclinic lysozyme at 0.65 A resolution.

Authors:  Jiawei Wang; Miroslawa Dauter; Randy Alkire; Andrzej Joachimiak; Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-11-16

7.  The atomic structure of the bluetongue virus core.

Authors:  J M Grimes; J N Burroughs; P Gouet; J M Diprose; R Malby; S Ziéntara; P P Mertens; D I Stuart
Journal:  Nature       Date:  1998-10-01       Impact factor: 49.962

8.  Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Authors: 
Journal:  J Mol Biol       Date:  1998-02-20       Impact factor: 5.469

Review 9.  Radiation damage in macromolecular cryocrystallography.

Authors:  Raimond B G Ravelli; Elspeth F Garman
Journal:  Curr Opin Struct Biol       Date:  2006-08-30       Impact factor: 6.809

10.  Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.

Authors:  E I Howard; R Sanishvili; R E Cachau; A Mitschler; B Chevrier; P Barth; V Lamour; M Van Zandt; E Sibley; C Bon; D Moras; T R Schneider; A Joachimiak; A Podjarny
Journal:  Proteins       Date:  2004-06-01
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  88 in total

1.  Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK.

Authors:  Natalie B Vinh; Jamie S Simpson; Peter J Scammells; David K Chalmers
Journal:  J Comput Aided Mol Des       Date:  2012-04-20       Impact factor: 3.686

2.  Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.

Authors:  Mark Berjanskii; Jianjun Zhou; Yongjie Liang; Guohui Lin; David S Wishart
Journal:  J Biomol NMR       Date:  2012-06-08       Impact factor: 2.835

3.  On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures.

Authors:  Andrew E Brereton; P Andrew Karplus
Journal:  Protein Sci       Date:  2016-02-08       Impact factor: 6.725

4.  Structural Analysis of Strigolactone-Related Gene Products.

Authors:  Inger Andersson; Gunilla H Carlsson; Dirk Hasse
Journal:  Methods Mol Biol       Date:  2021

5.  Problems in fitting high resolution structures into electron microscopic reconstructions.

Authors:  Edward H Egelman
Journal:  HFSP J       Date:  2008-09-29

6.  Data mining of metal ion environments present in protein structures.

Authors:  Heping Zheng; Maksymilian Chruszcz; Piotr Lasota; Lukasz Lebioda; Wladek Minor
Journal:  J Inorg Biochem       Date:  2008-05-28       Impact factor: 4.155

7.  The quality and validation of structures from structural genomics.

Authors:  Marcin J Domagalski; Heping Zheng; Matthew D Zimmerman; Zbigniew Dauter; Alexander Wlodawer; Wladek Minor
Journal:  Methods Mol Biol       Date:  2014

Review 8.  Determination of protein structures--a series of fortunate events.

Authors:  Maksymilian Chruszcz; Alexander Wlodawer; Wladek Minor
Journal:  Biophys J       Date:  2008-04-25       Impact factor: 4.033

Review 9.  Redox Signaling by Reactive Electrophiles and Oxidants.

Authors:  Saba Parvez; Marcus J C Long; Jesse R Poganik; Yimon Aye
Journal:  Chem Rev       Date:  2018-08-27       Impact factor: 60.622

10.  What are the current limits on determination of protonation state using neutron macromolecular crystallography?

Authors:  Dorothee Liebschner; Pavel V Afonine; Nigel W Moriarty; Paul D Adams
Journal:  Methods Enzymol       Date:  2020-02-13       Impact factor: 1.600

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