[Bioperl-guts-l] bioperl-network/t/data sulso_small.xml,NONE,1.1

Brian Osborne bosborne at dev.open-bio.org
Mon Jan 22 22:53:29 EST 2007


Update of /home/repository/bioperl/bioperl-network/t/data
In directory dev.open-bio.org:/tmp/cvs-serv23734

Added Files:
	sulso_small.xml 
Log Message:
Add small Sulfobolus file

--- NEW FILE: sulso_small.xml ---
   <entrySet level="2" minorVersion="3" version="5" xmlns="net:sf:psidev:mi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="net:sf:psidev:mi http://psidev.sourceforge.net/mi/rel25/src/MIF253.xsd">
     <entry>
       <source releaseDate="2007-01-12">
         <names>
           <shortLabel>European Bioinformatics Institute</shortLabel>
         </names>
         <bibref>
           <xref>
             <primaryRef db="pubmed" dbAc="MI:0446" id="14681455" refType="primary-reference" refTypeAc="MI:0358"/>
           </xref>
         </bibref>
         <xref>
           <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0469" refType="primary-reference" refTypeAc="MI:0358"/>
         </xref>
         <attributeList>
           <attribute name="postalAddress">Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom</attribute>
           <attribute name="url">http://www.ebi.ac.uk</attribute>
         </attributeList>
       </source>
       <experimentList>
         <experimentDescription id="2">
           <names>
             <shortLabel>knochel-1999-1</shortLabel>
             <fullName>The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications.</fullName>
           </names>
           <bibref>
             <xref>
               <primaryRef db="pubmed" dbAc="MI:0446" id="10449718" refType="primary-reference" refTypeAc="MI:0358"/>
             </xref>
           </bibref>
           <xref>
             <primaryRef db="intact" dbAc="MI:0469" id="EBI-1028078" secondary="knochel-1999-1"/>
             <secondaryRef db="newt" dbAc="MI:0247" id="2287" refType="target-species" secondary="sulso"/>
           </xref>
           <hostOrganismList>
             <hostOrganism ncbiTaxId="-1">
               <names>
                 <shortLabel>in vitro</shortLabel>
               </names>
             </hostOrganism>
           </hostOrganismList>
           <interactionDetectionMethod>
             <names>
               <shortLabel>x-ray</shortLabel>
               <fullName>x-ray crystallography</fullName>
               <alias>X-ray</alias>
             </names>
             <xref>
               <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0114" refType="identity" refTypeAc="MI:0356"/>
               <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
             </xref>
           </interactionDetectionMethod>
           <participantIdentificationMethod>
             <names>
               <shortLabel>predetermined</shortLabel>
               <fullName>predetermined participant</fullName>
             </names>
             <xref>
               <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0396" refType="identity" refTypeAc="MI:0356"/>
               <secondaryRef db="pubmed" dbAc="MI:0446" id="7940758" refType="go-definition-ref" refTypeAc="MI:0242"/>
               <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
             </xref>
           </participantIdentificationMethod>
           <attributeList>
             <attribute name="author-list">Knochel T., Ivens A., Hester G., Gonzalez A., Bauerle R., Wilmanns M., Kirschner K., Jansonius JN.</attribute>
             <attribute name="journal">Proc. Natl. Acad. Sci. U.S.A. (0027-8424)</attribute>
             <attribute name="publication-year">1999</attribute>
             <attribute name="dataset">MSD - Data obtained from The Macromolecular Structure Database</attribute>
           </attributeList>
         </experimentDescription>
       </experimentList>
       <interactorList>
         <interactor id="4">
           <names>
             <shortLabel>trpe_sulso</shortLabel>
             <fullName>Anthranilate synthase component 1</fullName>
             <alias type="gene name" typeAc="MI:0301">trpE</alias>
             <alias type="locus name" typeAc="MI:0305">SSO0893</alias>
           </names>
           <xref>
             <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q06128" refType="identity" refTypeAc="MI:0356" secondary="trpe_sulso" version="SP_56"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006805" secondary="Anth_synth_I_N"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR005801" secondary="TRPE_1_chor_bd"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR010116" secondary="TrpE_arc_synth"/>
             <secondaryRef db="intact" dbAc="MI:0469" id="EBI-1028059" secondary="trpe_sulso"/>
           </xref>
           <interactorType>
             <names>
               <shortLabel>protein</shortLabel>
               <fullName>protein</fullName>
             </names>
             <xref>
               <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
               <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
               <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="identity" refTypeAc="MI:0356"/>
             </xref>
           </interactorType>
           <organism ncbiTaxId="2287">
             <names>
               <shortLabel>sulso</shortLabel>
               <fullName>Sulfolobus solfataricus</fullName>
             </names>
           </organism>
           <sequence>MEVHPISEFASPFEVFKCIERDFKVAGLLESIGGPQYKARYSVIAWSTNGYLKIHDDPVNILNGYLKDLKLADIPGLFKGGMIGYISYDAVRFWEKIRDLKPAAEDWPYAEFFTPDNIIIYDHNEGKVYVNADLSSVGGCGDIGEFKVSFYDESLNKNSYERIVSESLEYIRSGYIFQVVLSRFYRYIFSGDPLRIYYNLRRINPSPYMFYLKFDEKYLIGSSPELLFRVQDNIVETYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHLMLVDLARNDLGKVCVPGTVKVPELMYVEKYSHVQHIVSKVIGTLKKKYNALNVLSATFPAGTVSGAPKPMAMNIIETLEEYKRGPYAGAVGFISADGNAEFAIAIRTAFLNKELLRIHAGAGIVYDSNPESEYFETEHKLKALKTAIGVR</sequence>
         </interactor>
         <interactor id="7">
           <names>
             <shortLabel>trpg_sulso</shortLabel>
             <fullName>Anthranilate synthase component II</fullName>
             <alias type="gene name" typeAc="MI:0301">trpG</alias>
             <alias type="locus name" typeAc="MI:0305">SSO0894</alias>
           </names>
           <xref>
             <primaryRef db="uniprotkb" dbAc="MI:0486" id="Q06129" refType="identity" refTypeAc="MI:0356" secondary="trpg_sulso" version="SP_52"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006220" secondary="Anth_synthII"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR001317" secondary="CP_synthGATase"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR011702" secondary="GATASE"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR000991" secondary="GATase_1"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR012998" secondary="GATase_1_AS"/>
             <secondaryRef db="interpro" dbAc="MI:0449" id="IPR006221" secondary="TrpG_papA"/>
             <secondaryRef db="intact" dbAc="MI:0469" id="EBI-1028067" secondary="trpg_sulso"/>
           </xref>
           <interactorType>
             <names>
               <shortLabel>protein</shortLabel>
               <fullName>protein</fullName>
             </names>
             <xref>
               <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0326" refType="identity" refTypeAc="MI:0356"/>
               <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
               <secondaryRef db="so" dbAc="MI:0601" id="SO:0000358" refType="identity" refTypeAc="MI:0356"/>
             </xref>
           </interactorType>
           <organism ncbiTaxId="2287">
             <names>
               <shortLabel>sulso</shortLabel>
               <fullName>Sulfolobus solfataricus</fullName>
             </names>
           </organism>
           <sequence>MDLTLIIDNYDSFVYNIAQIVGELGSYPIVIRNDEISIKGIERIDPDRIIISPGPGTPEKREDIGVSLDVIKYLGKRTPILGVCLGHQAIGYAFGAKIRRARKVFHGKISNIILVNNSPLSLYYGIAKEFKATRYHSLVVDEVHRPLIVDAISAEDNEIMAIHHEEYPIYGVQFHPESVGTSLGYKILYNFLNRV</sequence>
         </interactor>
       </interactorList>
       <interactionList>
         <interaction id="1">
           <names>
             <shortLabel>trpe-trpg-1</shortLabel>
             <fullName>The crystal structure of anthranilate synthase from
   sulfolobus solfataricus</fullName>
           </names>
           <xref>
             <primaryRef db="intact" dbAc="MI:0469" id="EBI-1028084" secondary="trpe-trpg-1"/>
             <secondaryRef db="pdb" dbAc="MI:0460" id="1QDL" refType="identity" refTypeAc="MI:0356"/>
           </xref>
           <experimentList>
             <experimentRef>2</experimentRef>
           </experimentList>
           <participantList>
             <participant id="3">
               <interactorRef>4</interactorRef>
               <biologicalRole>
                 <names>
                   <shortLabel>unspecified role</shortLabel>
                   <fullName>unspecified role</fullName>
                 </names>
                 <xref>
                   <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
                   <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
                 </xref>
               </biologicalRole>
               <experimentalRoleList>
                 <experimentalRole>
                   <names>
                     <shortLabel>neutral component</shortLabel>
                     <fullName>neutral component</fullName>
                   </names>
                   <xref>
                     <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0497" refType="identity" refTypeAc="MI:0356"/>
                     <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
                   </xref>
                 </experimentalRole>
               </experimentalRoleList>
               <featureList>
                 <feature id="5">
                   <names>
                     <shortLabel>region</shortLabel>
                   </names>
                   <featureType>
                     <names>
                       <shortLabel>sufficient to bind</shortLabel>
                       <fullName>sufficient binding site</fullName>
                     </names>
                     <xref>
                       <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0442" refType="identity" refTypeAc="MI:0356"/>
                       <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
                     </xref>
                   </featureType>
                   <featureRangeList>
                     <featureRange>
                       <startStatus>
                         <names>
                           <shortLabel>certain</shortLabel>
                         </names>
                         <xref>
                           <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
                         </xref>
                       </startStatus>
                       <begin position="1"/>
                       <endStatus>
                         <names>
                           <shortLabel>certain</shortLabel>
                         </names>
                         <xref>
                           <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
                         </xref>
                       </endStatus>
                       <end position="421"/>
                     </featureRange>
                   </featureRangeList>
                 </feature>
               </featureList>
               <hostOrganismList>
                 <hostOrganism ncbiTaxId="2287">
                   <names>
                     <shortLabel>sulso</shortLabel>
                     <fullName>Sulfolobus solfataricus</fullName>
                   </names>
                 </hostOrganism>
               </hostOrganismList>
             </participant>
             <participant id="6">
               <interactorRef>7</interactorRef>
               <biologicalRole>
                 <names>
                   <shortLabel>unspecified role</shortLabel>
                   <fullName>unspecified role</fullName>
                 </names>
                 <xref>
                   <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0499" refType="identity" refTypeAc="MI:0356"/>
                   <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
                 </xref>
               </biologicalRole>
               <experimentalRoleList>
                 <experimentalRole>
                   <names>
                     <shortLabel>neutral component</shortLabel>
                     <fullName>neutral component</fullName>
                   </names>
                   <xref>
                     <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0497" refType="identity" refTypeAc="MI:0356"/>
                     <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
                   </xref>
                 </experimentalRole>
               </experimentalRoleList>
               <featureList>
                 <feature id="8">
                   <names>
                     <shortLabel>region</shortLabel>
                   </names>
                   <featureType>
                     <names>
                       <shortLabel>sufficient to bind</shortLabel>
                       <fullName>sufficient binding site</fullName>
                     </names>
                     <xref>
                       <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0442" refType="identity" refTypeAc="MI:0356"/>
                       <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
                     </xref>
                   </featureType>
                   <featureRangeList>
                     <featureRange>
                       <startStatus>
                         <names>
                           <shortLabel>certain</shortLabel>
                         </names>
                         <xref>
                           <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
                         </xref>
                       </startStatus>
                       <begin position="1"/>
                       <endStatus>
                         <names>
                           <shortLabel>certain</shortLabel>
                         </names>
                         <xref>
                           <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0335" refType="identity" refTypeAc="MI:0356"/>
                         </xref>
                       </endStatus>
                       <end position="195"/>
                     </featureRange>
                   </featureRangeList>
                 </feature>
               </featureList>
               <hostOrganismList>
                 <hostOrganism ncbiTaxId="2287">
                   <names>
                     <shortLabel>sulso</shortLabel>
                     <fullName>Sulfolobus solfataricus</fullName>
                   </names>
                 </hostOrganism>
               </hostOrganismList>
             </participant>
           </participantList>
           <interactionType>
             <names>
               <shortLabel>direct interaction</shortLabel>
               <fullName>direct interaction</fullName>
             </names>
             <xref>
               <primaryRef db="psi-mi" dbAc="MI:0488" id="MI:0407" refType="identity" refTypeAc="MI:0356"/>
               <secondaryRef db="pubmed" dbAc="MI:0446" id="14755292" refType="primary-reference" refTypeAc="MI:0358"/>
             </xref>
           </interactionType>
           <attributeList>
             <attribute name="assembly">tetrameric, multimeric</attribute>
             <attribute name="3d-r-factors">working 77.400%, free 74.600%</attribute>
             <attribute name="3d-resolution">2.5A</attribute>
           </attributeList>
         </interaction>
       </interactionList>
     </entry>
   </entrySet>



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