Phaser.MRage: automated molecular replacement

Bunkóczi, Gábor; Echols, Nathaniel; McCoy, Airlie J.; Oeffner, Robert D.; Adams, Paul D.

doi:10.1107/S0907444913022750

Title: Phaser.MRage: automated molecular replacement

Journal Article · Fri Nov 01 00:00:00 EDT 2013 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S0907444913022750· OSTI ID:22347840

Bunkóczi, Gábor ^[1]; Echols, Nathaniel ^[2]; McCoy, Airlie J.; Oeffner, Robert D. ^[1]; Adams, Paul D. ^[2]

University of Cambridge, CIMR, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY (United Kingdom)
Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64R0121, Berkeley, CA 94720 (United States)

The functionality of the molecular-replacement pipeline phaser.MRage is introduced and illustrated with examples. Phaser.MRage is a molecular-replacement automation framework that implements a full model-generation workflow and provides several layers of model exploration to the user. It is designed to handle a large number of models and can distribute calculations efficiently onto parallel hardware. In addition, phaser.MRage can identify correct solutions and use this information to accelerate the search. Firstly, it can quickly score all alternative models of a component once a correct solution has been found. Secondly, it can perform extensive analysis of identified solutions to find protein assemblies and can employ assembled models for subsequent searches. Thirdly, it is able to use a priori assembly information (derived from, for example, homologues) to speculatively place and score molecules, thereby customizing the search procedure to a certain class of protein molecule (for example, antibodies) and incorporating additional biological information into molecular replacement.

Cite

Export

Save

OSTI ID:: 22347840

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography, Vol. 69, Issue Pt 11; Other Information: PMCID: PMC3817702; PMID: 24189240; PUBLISHER-ID: ba5210; OAI: oai:pubmedcentral.nih.gov:3817702; Copyright (c) Bunkóczi et al. 2013; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449

Country of Publication:: Denmark

Language:: English

References (23)

The relation between the divergence of sequence and structure in proteins. Chothia, C.; Lesk, A. M. The EMBO Journal, Vol. 5, Issue 4 https://doi.org/10.1002/j.1460-2075.1986.tb04288.x	journal	April 1986
Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8 Sakai, Hiroaki; Vassylyeva, Marina N.; Matsuura, Takanori Journal of Molecular Biology, Vol. 332, Issue 3 https://doi.org/10.1016/s0022-2836(03)00946-x	journal	September 2003
Structure of the Shiga-like Toxin I B-Pentamer Complexed with an Analogue of Its Receptor Gb ₃ ^† ^, ^‡ Ling, Hong; Boodhoo, Amechand; Hazes, Bart Biochemistry, Vol. 37, Issue 7 https://doi.org/10.1021/bi971806n	journal	February 1998
Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli Stein, Penelope E.; Boodhoo, Amechand; Tyrrell, Gregory J. Nature, Vol. 355, Issue 6362 https://doi.org/10.1038/355748a0	journal	February 1992
Improved molecular replacement by density- and energy-guided protein structure optimization DiMaio, Frank; Terwilliger, Thomas C.; Read, Randy J. Nature, Vol. 473, Issue 7348 https://doi.org/10.1038/nature09964	journal	May 2011
Announcing the worldwide Protein Data Bank Berman, Helen; Henrick, Kim; Nakamura, Haruki Nature Structural & Molecular Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nsb1203-980	journal	December 2003
Crystal structure of a clip-domain serine protease and functional roles of the clip domains Piao, Shunfu; Song, Young-Lan; Kim, Jung Hyun The EMBO Journal, Vol. 24, Issue 24 https://doi.org/10.1038/sj.emboj.7600891	journal	December 2005
Protein structure determination by exhaustive search of Protein Data Bank derived databases Stokes-Rees, I.; Sliz, P. Proceedings of the National Academy of Sciences, Vol. 107, Issue 50 https://doi.org/10.1073/pnas.1012095107	journal	November 2010
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
The HHpred interactive server for protein homology detection and structure prediction Soding, J.; Biegert, A.; Lupas, A. N. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki408	journal	July 2005
FFAS03: a server for profile-profile sequence alignments Jaroszewski, L.; Rychlewski, L.; Li, Z. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki418	journal	July 2005
Atomic resolution structures of trypsin provide insight into structural radiation damage Leiros, Hanna-Kirsti Schrøder; McSweeney, Seán M.; Smalås, Arne O. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 4 https://doi.org/10.1107/s0907444901000646	journal	April 2001
Evaluating the solution from MrBUMP and BALBES Keegan, Ronan M.; Long, Fei; Fazio, Vincent J. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s0907444911007530	journal	March 2011
AMPLE : a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 12 https://doi.org/10.1107/s0907444912039194	journal	November 2012
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Complete Genome Sequence of Clostridium botulinum CJ0611A1, a Type A(B) Isolate Associated with an International Outbreak of Botulism from Commercial Carrot Juice Harris, Richard; Dussault, Forest; Flint, Annika Microbiology Resource Announcements, Vol. 10, Issue 1 https://doi.org/10.1128/mra.01111-20	journal	January 2021
Graphical tools for macromolecular crystallography in PHENIX. Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.52318	text	January 2012
Overview of the CCP4 suite and current developments. Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.52322	text	January 2011
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. International Union of Crystallography (IUCr) https://doi.org/10.17863/cam.52329	journalarticle	January 2008
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Improvement of molecular-replacement models with Sculptor. Bunkóczi, Gábor; Read, Randy J. International Union of Crystallography (IUCr) https://doi.org/10.17863/cam.52324	journalarticle	January 2011

Cited By (49)

Dodecameric structure of a small heat shock protein from Mycobacterium marinum M Bhandari, Spraha; Biswas, Sreeparna; Chaudhary, Anuradha Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 5 https://doi.org/10.1002/prot.25657	journal	January 2019
X-ray structures and mechanism of the human serotonin transporter Coleman, Jonathan A.; Green, Evan M.; Gouaux, Eric Nature, Vol. 532, Issue 7599 https://doi.org/10.1038/nature17629	journal	April 2016
Structural and functional insights into IZUMO1 recognition by JUNO in mammalian fertilization Kato, Kazuki; Satouh, Yuhkoh; Nishimasu, Hiroshi Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12198	journal	July 2016
Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain Gumiero, Andrea; Conz, Charlotte; Gesé, Genís Valentín Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13563	journal	November 2016
Structural basis of HypK regulating N-terminal acetylation by the NatA complex Weyer, Felix Alexander; Gumiero, Andrea; Lapouge, Karine Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15726	journal	June 2017
The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis Feng, Han; Liu, Xuehui; Wang, Sheng Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02339-w	journal	December 2017
The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development Schumacher, Maria A.; den Hengst, Chris D.; Bush, Matthew J. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03576-3	journal	March 2018
Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01 Gu, Yue; Wong, Yee Hwa; Liew, Chong Wai Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-08790-1	journal	February 2019
Structural basis for recognition of diverse antidepressants by the human serotonin transporter Coleman, Jonathan A.; Gouaux, Eric Nature Structural & Molecular Biology, Vol. 25, Issue 2 https://doi.org/10.1038/s41594-018-0026-8	journal	January 2018
Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis Barruetabeña, Nerea; Alonso-Lerma, Borja; Galera-Prat, Albert Communications Chemistry, Vol. 2, Issue 1 https://doi.org/10.1038/s42004-019-0176-6	journal	July 2019
Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA Chen, Minghao; Asai, Shin-ichi; Narai, Shun Proceedings of the National Academy of Sciences, Vol. 114, Issue 19 https://doi.org/10.1073/pnas.1615585114	journal	April 2017
Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55 Gao, Chen; Pallett, Mitchell A.; Croll, Tristan I. Journal of Biological Chemistry, Vol. 294, Issue 16 https://doi.org/10.1074/jbc.ra118.006561	journal	February 2019
Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease Taylor, Hannah N.; Warner, Emily E.; Armbrust, Matthew J. RNA Biology, Vol. 16, Issue 10 https://doi.org/10.1080/15476286.2019.1634965	journal	June 2019
The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex Schumacher, Maria A.; Zeng, Wenjie; Findlay, Kim C. Nucleic Acids Research, Vol. 45, Issue 11 https://doi.org/10.1093/nar/gkx287	journal	April 2017
A folded conformation of MukBEF and Cohesin Bürmann, Frank; Lee, Byung-Gil; Than, Thane bioRxiv https://doi.org/10.1101/464701	posted_content	January 2018
New crystal form of human ubiquitin in the presence of magnesium Camara-Artigas, Ana; Plaza-Garrido, Marina; Martinez-Rodriguez, Sergio Acta Crystallographica Section F Structural Biology Communications, Vol. 72, Issue 1 https://doi.org/10.1107/s2053230x15023390	journal	January 2016
Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content Salinas-Garcia, M. Carmen; Plaza-Garrido, Marina; Alba-Elena, Daniel Acta Crystallographica Section F Structural Biology Communications, Vol. 75, Issue 11 https://doi.org/10.1107/s2053230x19013189	journal	November 2019
Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination Millán, Claudia; Sammito, Massimo Domenico; McCoy, Airlie J. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 4 https://doi.org/10.1107/s2059798318001365	journal	April 2018
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE Rigden, Daniel J.; Thomas, Jens M. H.; Simkovic, Felix Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 3 https://doi.org/10.1107/s2059798318002310	journal	March 2018
Recent developments in MrBUMP : better search-model preparation, graphical interaction with search models, and solution improvement and assessment Keegan, Ronan M.; McNicholas, Stuart J.; Thomas, Jens M. H. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 3 https://doi.org/10.1107/s2059798318003455	journal	March 2018
Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95 Camara-Artigas, Ana; Murciano-Calles, Javier; Martínez, Jose C. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 4 https://doi.org/10.1107/s2059798319001980	journal	March 2019
A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad Kumar, Prashasti; Serpersu, Engin H.; Cuneo, Matthew J. Science Advances, Vol. 4, Issue 4 https://doi.org/10.1126/sciadv.aas8667	journal	April 2018
Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio Titov, D. V.; Cracan, V.; Goodman, R. P. Science, Vol. 352, Issue 6282 https://doi.org/10.1126/science.aad4017	journal	April 2016
Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition Ballinger, Elaine; Mosior, John; Hartman, Travis Science, Vol. 363, Issue 6426 https://doi.org/10.1126/science.aau8959	journal	January 2019
Homodimerization attenuates the anti-inflammatory activity of interleukin-37 Ellisdon, Andrew M.; Nold-Petry, Claudia A.; D’Andrea, Laura Science Immunology, Vol. 2, Issue 8 https://doi.org/10.1126/sciimmunol.aaj1548	journal	February 2017
Cyclic Boronates Inhibit All Classes of β-Lactamases Cahill, Samuel T.; Cain, Ricky; Wang, David Y. Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 4 https://doi.org/10.1128/aac.02260-16	journal	January 2017
Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation Bacarizo, Julio; Martinez-Rodriguez, Sergio; Martin-Garcia, Jose Manuel PLoS ONE, Vol. 9, Issue 12 https://doi.org/10.1371/journal.pone.0113224	journal	December 2014
Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase Berndt, Sandra; Gurevich, Vsevolod V.; Iverson, T. M. PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0215140	journal	April 2019
Epsin and Sla2 form assemblies through phospholipid interfaces Garcia-Alai, Maria M.; Heidemann, Johannes; Skruzny, Michal Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-05255	text	January 2018
In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors Nass, Karol; Redecke, Lars; Perbandt, Markus Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2020-00621	text	January 2020
A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion Annia, Rodríguez-Hernández; Romo-Arévalo, Enrique; Rodríguez-Romero, Adela Crystals, Vol. 9, Issue 12 https://doi.org/10.3390/cryst9120622	journal	November 2019
Epsin and Sla2 form assemblies through phospholipid interfaces Garcia-Alai, Maria M.; Heidemann, Johannes; Skruzny, Michal Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02443-x	journal	January 2018
A folded conformation of MukBEF and cohesin Bürmann, Frank; Lee, Byung-Gil; Than, Thane Nature Structural & Molecular Biology, Vol. 26, Issue 3 https://doi.org/10.1038/s41594-019-0196-z	journal	March 2019
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43042	text	January 2019
Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease Taylor, H. N.; Warner, E. E.; Armbrust, M. J. Taylor & Francis https://doi.org/10.6084/m9.figshare.8312441.v1	text	January 2019
In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors Nass, Karol; Redecke, Lars; Perbandt, M. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14484-w	journal	January 2020
Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination. Millán, Claudia; Sammito, Massimo; McCoy, Airlie Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.25122	text	January 2018
Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55. Gao, Chen; Pallett, Mitchell A.; Croll, Tristan Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.37397	text	January 2019
Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease Taylor, Hannah N.; Warner, Emily E.; Armbrust, Matthew J. Taylor & Francis https://doi.org/10.6084/m9.figshare.8312441.v3	text	January 2019
Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC Liu, Ying; Bhowmick, Tuhin; Liu, Yiqiong Neuron, Vol. 97, Issue 6 https://doi.org/10.1016/j.neuron.2018.02.010	journal	March 2018
A tight tunable range for Ni(II) sensing and buffering in cells Foster, Andrew W.; Pernil, Rafael; Patterson, Carl J. Nature Chemical Biology, Vol. 13, Issue 4 https://doi.org/10.1038/nchembio.2310	journal	February 2017
Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase Muraki, Norifumi; Ishii, Kentaro; Uchiyama, Susumu Communications Biology, Vol. 2, Issue 1 https://doi.org/10.1038/s42003-019-0631-z	journal	October 2019
Structural basis for recognition of Emi2 by Polo-like kinase 1 and development of peptidomimetics blocking oocyte maturation and fertilization Jia, Jia-Lin; Han, Young-Hyun; Kim, Hak-Cheol Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14626	journal	October 2015
Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity Kumar, Pankaj; Magala, Pearl; Geiger-Schuller, Kathryn R. Nucleic Acids Research, Vol. 43, Issue 18 https://doi.org/10.1093/nar/gkv845	journal	August 2015
A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication Wu, Chyuan-Chuan; Lin, Jason L. J.; Yang-Yen, Hsin-Fang Nucleic Acids Research, Vol. 47, Issue 10 https://doi.org/10.1093/nar/gkz241	journal	April 2019
Recognition and processing of branched DNA substrates by Slx1–Slx4 nuclease Gaur, Vineet; Ziajko, Weronika; Nirwal, Shivlee Nucleic Acids Research, Vol. 47, Issue 22 https://doi.org/10.1093/nar/gkz842	journal	October 2019
Antibiotic Capture by Bacterial Lipocalins Uncovers an Extracellular Mechanism of Intrinsic Antibiotic Resistance El-Halfawy, Omar M.; Klett, Javier; Ingram, Rebecca J. mBio, Vol. 8, Issue 2 https://doi.org/10.1128/mbio.00225-17	journal	May 2017
Symmetry based assembly of a 2 dimensional protein lattice Poulos, Sandra; Agah, Sayeh; Jallah, Nikardi PLOS ONE, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pone.0174485	journal	April 2017
Structural determination of the complement inhibitory domain of Borrelia burgdorferi BBK32 provides insight into classical pathway complement evasion by Lyme disease spirochetes Xie, Jialei; Zhi, Hui; Garrigues, Ryan J. PLOS Pathogens, Vol. 15, Issue 3 https://doi.org/10.1371/journal.ppat.1007659	journal	March 2019

Similar Records

Phaser.MRage: automated molecular replacement

Journal Article · Fri Oct 18 00:00:00 EDT 2013 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:22347840

Bunkóczi, Gábor; Echols, Nathaniel; McCoy, Airlie J.; +3 more

Molecular replacement: tricks and treats

Journal Article · Fri Nov 01 00:00:00 EDT 2013 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:22347840

Abergel, Chantal

TOPITS: Threading one-dimensional predictions into three-dimensional structures

Technical Report · Sun Dec 31 00:00:00 EST 1995 · OSTI ID:22347840

Rost, B

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
LAYERS
MATHEMATICAL SOLUTIONS
MOLECULES
PROTEINS
SOLUTIONS

Title: Phaser.MRage: automated molecular replacement

Citation Formats

References (23)

Cited By (49)

Similar Records

Related Subjects