Loading…
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367
The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal stru...
Saved in:
| Published in: | Acta crystallographica. Section F, Structural biology and crystallization communications Structural biology and crystallization communications, 2010-10, Vol.66 (10), p.1381-1392 |
|---|---|
| Main Authors: | , , , , , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c6073-59ae05c961a541cea8c3fe0a594a9422c82b852251be058dbd0f7772607a4a2f3 |
|---|---|
| cites | |
| container_end_page | 1392 |
| container_issue | 10 |
| container_start_page | 1381 |
| container_title | Acta crystallographica. Section F, Structural biology and crystallization communications |
| container_volume | 66 |
| creator | Mohanty, Biswaranjan Serrano, Pedro Pedrini, Bill Jaudzems, Kristaps Geralt, Michael Horst, Reto Herrmann, Torsten Elsliger, Marc-André Wilson, Ian A. Wüthrich, Kurt |
| description | The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of |
| doi_str_mv | 10.1107/S1744309110020956 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2954229</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3859667451</sourcerecordid><originalsourceid>FETCH-LOGICAL-c6073-59ae05c961a541cea8c3fe0a594a9422c82b852251be058dbd0f7772607a4a2f3</originalsourceid><addsrcrecordid>eNqFkUtvEzEURi0E6vsHsEEWLFgN-Dkeb5CqlCaIPgSURqwsx_EQl4md2p5C_j0OU6ICC1a2r893_LgAPMXoFcZIvP6EBWMUybJABElePwJ7m1K1qT1-MN8F-yndIESprJsdsFtgxgjle-D9KCxXOroUPAwtvDj_CLWfQxPXKesOphx7k_toE2xDhHlh4SqGbJ1P8OocY0x-4WVKa3EInrS6S_bofjwAn0_fXo0m1dnl-N3o-KwyNRK04lJbxI2sseYMG6sbQ1uLNJdMS0aIacis4YRwPCtcM5_NUSuEICWsmSYtPQBvBu-qny3t3Fifo-7UKrqljmsVtFN_7ni3UF_DnSKSF78sgueDIKTsVDIuW7MwwXtrssI14UI2BXp5f0oMt71NWS1dMrbrtLehT0rwpqG05qyQL_4ib0IfffkChQUtPkzJxocHysSQUrTt9sIYqU071T_tLJlnD1-6TfzuXwHkAHx3nV3_36iOv5yS6QnHlJZsNWRdyvbHNqvjN1ULKriaXozVePKBXl9PkJrSnyIMttg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1731621328</pqid></control><display><type>article</type><title>Comparison of NMR and crystal structures for the proteins TM1112 and TM1367</title><source>Open Access: PubMed Central</source><source>Wiley-Blackwell Read & Publish Collection</source><creator>Mohanty, Biswaranjan ; Serrano, Pedro ; Pedrini, Bill ; Jaudzems, Kristaps ; Geralt, Michael ; Horst, Reto ; Herrmann, Torsten ; Elsliger, Marc-André ; Wilson, Ian A. ; Wüthrich, Kurt</creator><creatorcontrib>Mohanty, Biswaranjan ; Serrano, Pedro ; Pedrini, Bill ; Jaudzems, Kristaps ; Geralt, Michael ; Horst, Reto ; Herrmann, Torsten ; Elsliger, Marc-André ; Wilson, Ian A. ; Wüthrich, Kurt ; The Scripps Research Inst., La Jolla, CA (United States)</creatorcontrib><description>The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper‐limit distance constraints derived from the molecular models that represent the results of structure determination by NMR and by X‐ray diffraction, respectively. The results thus obtained show that NMR structure calculations with the new automated UNIO software used by the JCSG compare favorably with those from a more labor‐intensive and time‐intensive interactive procedure. An intriguing observation is that the `bundles' of two TM1112 or three TM1367 molecules in the asymmetric unit of the crystal structures mimic the behavior of the bundles of 20 conformers used to represent the NMR solution structures when comparing global r.m.s.d. values calculated either for the polypeptide backbone, the core residues with solvent accessibility below 15% or all heavy atoms.</description><identifier>ISSN: 1744-3091</identifier><identifier>EISSN: 1744-3091</identifier><identifier>EISSN: 2053-230X</identifier><identifier>DOI: 10.1107/S1744309110020956</identifier><identifier>PMID: 20944235</identifier><language>eng</language><publisher>5 Abbey Square, Chester, Cheshire CH1 2HU, England: International Union of Crystallography</publisher><subject>Amino Acid Sequence ; Bacterial Proteins - chemistry ; BASIC BIOLOGICAL SCIENCES ; Biochemistry & Molecular Biology ; Biophysics ; Crystallography ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; NMR and crystal structure comparison ; NMR in a high-throughput environment ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Tertiary ; reference structures ; Structural Homology, Protein ; structure-determination software ; Thermotoga maritima ; Thermotoga maritima - chemistry</subject><ispartof>Acta crystallographica. Section F, Structural biology and crystallization communications, 2010-10, Vol.66 (10), p.1381-1392</ispartof><rights>Mohanty et al. 2010</rights><rights>Mohanty et al. 2010</rights><rights>Mohanty et al. 2010 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6073-59ae05c961a541cea8c3fe0a594a9422c82b852251be058dbd0f7772607a4a2f3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954229/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954229/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20944235$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1625798$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Mohanty, Biswaranjan</creatorcontrib><creatorcontrib>Serrano, Pedro</creatorcontrib><creatorcontrib>Pedrini, Bill</creatorcontrib><creatorcontrib>Jaudzems, Kristaps</creatorcontrib><creatorcontrib>Geralt, Michael</creatorcontrib><creatorcontrib>Horst, Reto</creatorcontrib><creatorcontrib>Herrmann, Torsten</creatorcontrib><creatorcontrib>Elsliger, Marc-André</creatorcontrib><creatorcontrib>Wilson, Ian A.</creatorcontrib><creatorcontrib>Wüthrich, Kurt</creatorcontrib><creatorcontrib>The Scripps Research Inst., La Jolla, CA (United States)</creatorcontrib><title>Comparison of NMR and crystal structures for the proteins TM1112 and TM1367</title><title>Acta crystallographica. Section F, Structural biology and crystallization communications</title><addtitle>Acta Cryst. F</addtitle><description>The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper‐limit distance constraints derived from the molecular models that represent the results of structure determination by NMR and by X‐ray diffraction, respectively. The results thus obtained show that NMR structure calculations with the new automated UNIO software used by the JCSG compare favorably with those from a more labor‐intensive and time‐intensive interactive procedure. An intriguing observation is that the `bundles' of two TM1112 or three TM1367 molecules in the asymmetric unit of the crystal structures mimic the behavior of the bundles of 20 conformers used to represent the NMR solution structures when comparing global r.m.s.d. values calculated either for the polypeptide backbone, the core residues with solvent accessibility below 15% or all heavy atoms.</description><subject>Amino Acid Sequence</subject><subject>Bacterial Proteins - chemistry</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biochemistry & Molecular Biology</subject><subject>Biophysics</subject><subject>Crystallography</subject><subject>Crystallography, X-Ray</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>NMR and crystal structure comparison</subject><subject>NMR in a high-throughput environment</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Protein Structure, Tertiary</subject><subject>reference structures</subject><subject>Structural Homology, Protein</subject><subject>structure-determination software</subject><subject>Thermotoga maritima</subject><subject>Thermotoga maritima - chemistry</subject><issn>1744-3091</issn><issn>1744-3091</issn><issn>2053-230X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNqFkUtvEzEURi0E6vsHsEEWLFgN-Dkeb5CqlCaIPgSURqwsx_EQl4md2p5C_j0OU6ICC1a2r893_LgAPMXoFcZIvP6EBWMUybJABElePwJ7m1K1qT1-MN8F-yndIESprJsdsFtgxgjle-D9KCxXOroUPAwtvDj_CLWfQxPXKesOphx7k_toE2xDhHlh4SqGbJ1P8OocY0x-4WVKa3EInrS6S_bofjwAn0_fXo0m1dnl-N3o-KwyNRK04lJbxI2sseYMG6sbQ1uLNJdMS0aIacis4YRwPCtcM5_NUSuEICWsmSYtPQBvBu-qny3t3Fifo-7UKrqljmsVtFN_7ni3UF_DnSKSF78sgueDIKTsVDIuW7MwwXtrssI14UI2BXp5f0oMt71NWS1dMrbrtLehT0rwpqG05qyQL_4ib0IfffkChQUtPkzJxocHysSQUrTt9sIYqU071T_tLJlnD1-6TfzuXwHkAHx3nV3_36iOv5yS6QnHlJZsNWRdyvbHNqvjN1ULKriaXozVePKBXl9PkJrSnyIMttg</recordid><startdate>201010</startdate><enddate>201010</enddate><creator>Mohanty, Biswaranjan</creator><creator>Serrano, Pedro</creator><creator>Pedrini, Bill</creator><creator>Jaudzems, Kristaps</creator><creator>Geralt, Michael</creator><creator>Horst, Reto</creator><creator>Herrmann, Torsten</creator><creator>Elsliger, Marc-André</creator><creator>Wilson, Ian A.</creator><creator>Wüthrich, Kurt</creator><general>International Union of Crystallography</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope><scope>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>201010</creationdate><title>Comparison of NMR and crystal structures for the proteins TM1112 and TM1367</title><author>Mohanty, Biswaranjan ; Serrano, Pedro ; Pedrini, Bill ; Jaudzems, Kristaps ; Geralt, Michael ; Horst, Reto ; Herrmann, Torsten ; Elsliger, Marc-André ; Wilson, Ian A. ; Wüthrich, Kurt</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6073-59ae05c961a541cea8c3fe0a594a9422c82b852251be058dbd0f7772607a4a2f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Amino Acid Sequence</topic><topic>Bacterial Proteins - chemistry</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Biochemistry & Molecular Biology</topic><topic>Biophysics</topic><topic>Crystallography</topic><topic>Crystallography, X-Ray</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>NMR and crystal structure comparison</topic><topic>NMR in a high-throughput environment</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>Protein Structure, Tertiary</topic><topic>reference structures</topic><topic>Structural Homology, Protein</topic><topic>structure-determination software</topic><topic>Thermotoga maritima</topic><topic>Thermotoga maritima - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mohanty, Biswaranjan</creatorcontrib><creatorcontrib>Serrano, Pedro</creatorcontrib><creatorcontrib>Pedrini, Bill</creatorcontrib><creatorcontrib>Jaudzems, Kristaps</creatorcontrib><creatorcontrib>Geralt, Michael</creatorcontrib><creatorcontrib>Horst, Reto</creatorcontrib><creatorcontrib>Herrmann, Torsten</creatorcontrib><creatorcontrib>Elsliger, Marc-André</creatorcontrib><creatorcontrib>Wilson, Ian A.</creatorcontrib><creatorcontrib>Wüthrich, Kurt</creatorcontrib><creatorcontrib>The Scripps Research Inst., La Jolla, CA (United States)</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Acta crystallographica. Section F, Structural biology and crystallization communications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mohanty, Biswaranjan</au><au>Serrano, Pedro</au><au>Pedrini, Bill</au><au>Jaudzems, Kristaps</au><au>Geralt, Michael</au><au>Horst, Reto</au><au>Herrmann, Torsten</au><au>Elsliger, Marc-André</au><au>Wilson, Ian A.</au><au>Wüthrich, Kurt</au><aucorp>The Scripps Research Inst., La Jolla, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of NMR and crystal structures for the proteins TM1112 and TM1367</atitle><jtitle>Acta crystallographica. Section F, Structural biology and crystallization communications</jtitle><addtitle>Acta Cryst. F</addtitle><date>2010-10</date><risdate>2010</risdate><volume>66</volume><issue>10</issue><spage>1381</spage><epage>1392</epage><pages>1381-1392</pages><issn>1744-3091</issn><eissn>1744-3091</eissn><eissn>2053-230X</eissn><abstract>The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper‐limit distance constraints derived from the molecular models that represent the results of structure determination by NMR and by X‐ray diffraction, respectively. The results thus obtained show that NMR structure calculations with the new automated UNIO software used by the JCSG compare favorably with those from a more labor‐intensive and time‐intensive interactive procedure. An intriguing observation is that the `bundles' of two TM1112 or three TM1367 molecules in the asymmetric unit of the crystal structures mimic the behavior of the bundles of 20 conformers used to represent the NMR solution structures when comparing global r.m.s.d. values calculated either for the polypeptide backbone, the core residues with solvent accessibility below 15% or all heavy atoms.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>International Union of Crystallography</pub><pmid>20944235</pmid><doi>10.1107/S1744309110020956</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1744-3091 |
| ispartof | Acta crystallographica. Section F, Structural biology and crystallization communications, 2010-10, Vol.66 (10), p.1381-1392 |
| issn | 1744-3091 1744-3091 2053-230X |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2954229 |
| source | Open Access: PubMed Central; Wiley-Blackwell Read & Publish Collection |
| subjects | Amino Acid Sequence Bacterial Proteins - chemistry BASIC BIOLOGICAL SCIENCES Biochemistry & Molecular Biology Biophysics Crystallography Crystallography, X-Ray Models, Molecular Molecular Sequence Data NMR and crystal structure comparison NMR in a high-throughput environment Nuclear Magnetic Resonance, Biomolecular Protein Structure, Tertiary reference structures Structural Homology, Protein structure-determination software Thermotoga maritima Thermotoga maritima - chemistry |
| title | Comparison of NMR and crystal structures for the proteins TM1112 and TM1367 |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-27T04%3A00%3A25IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparison%20of%20NMR%20and%20crystal%20structures%20for%20the%20proteins%20TM1112%20and%20TM1367&rft.jtitle=Acta%20crystallographica.%20Section%20F,%20Structural%20biology%20and%20crystallization%20communications&rft.au=Mohanty,%20Biswaranjan&rft.aucorp=The%20Scripps%20Research%20Inst.,%20La%20Jolla,%20CA%20(United%20States)&rft.date=2010-10&rft.volume=66&rft.issue=10&rft.spage=1381&rft.epage=1392&rft.pages=1381-1392&rft.issn=1744-3091&rft.eissn=1744-3091&rft_id=info:doi/10.1107/S1744309110020956&rft_dat=%3Cproquest_pubme%3E3859667451%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c6073-59ae05c961a541cea8c3fe0a594a9422c82b852251be058dbd0f7772607a4a2f3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1731621328&rft_id=info:pmid/20944235&rfr_iscdi=true |