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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOTOSENSORY CORE MODULE OF BACTERIOPHYTOCHROME RPA3015 FROM R. PALUSTRIS
 
Authors :  X. Yang, E. A. Stojkovi, W. B. Ozarowski, K. Moffat
Date :  17 Jan 15  (Deposition) - 15 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pas Fold, Transferase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Yang, E. A. Stojkovic, W. B. Ozarowski, J. Kuk, E. Davydova, K. Moffa
Light Signaling Mechanism Of Two Tandem Bacteriophytochromes.
Structure V. 23 1179 2015
PubMed-ID: 26095026  |  Reference-DOI: 10.1016/J.STR.2015.04.022

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME (LIGHT-REGULATED SIGNAL TRANSDUCTION HISTIDINE KINASE), PHYB1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 1-505
    Gene: PHYB1, RPA3015
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS CGA009
    Organism Taxid: 258594
    Strain: CGA009
    Synonym: PHOTOSENSORY CORE MODULE OF BACTERIOPHYTOCHROME RPA3015 (RPBPHP2)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1BLA2Ligand/IonBILIVERDINE IX ALPHA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , GLU A:18 , ILE A:20 , MET A:169 , TYR A:171 , PHE A:198 , ASP A:202 , ILE A:203 , PRO A:204 , TYR A:211 , ARG A:249 , VAL A:251 , SER A:252 , VAL A:254 , HIS A:255 , TYR A:258 , MET A:259 , THR A:267 , SER A:269 , HIS A:285 , HOH A:1001BINDING SITE FOR RESIDUE BLA A 900
2AC2SOFTWARECYS B:15 , MET B:169 , SER B:201 , ASP B:202 , ILE B:203 , PRO B:204 , TYR B:211 , ARG B:217 , ARG B:249 , VAL B:251 , SER B:252 , VAL B:254 , HIS B:255 , TYR B:258 , THR B:267 , MET B:268 , SER B:269 , ALA B:283 , HIS B:285 , ARG B:466BINDING SITE FOR RESIDUE BLA B 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S21)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:89 -Pro A:90
2Thr A:230 -Pro A:231
3Pro A:430 -Pro A:431
4Gly A:450 -Asn A:451
5Thr B:230 -Pro B:231
6Lys B:325 -Gly B:326
7Thr B:429 -Pro B:430
8Pro B:430 -Pro B:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S21)

(-) Exons   (0, 0)

(no "Exon" information available for 4S21)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.......ee....eeeee.....eeeee..hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh......ee........eeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........ee.....hhhhhhhhh...eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...eeeee....eeee........hhhhhh..........eee......hhhhhh......eeeeee........eeeeee.....eeeee................eeeee........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s21 A  13 STCDDEPIHIPGAIQPHGLLLALAADMTIVAGSDNLPELTGLAIGALIGRSAADVFDSETHNRLTIALAEPGAPIAVGFTDAGFVGSWHRHDQLVFLELEPPPQAFFRRTNSAIRRLQAAETLESACAAAAQEVREITGFDRVMIYRFASDFSGEVIAEDRCAEVESYLGLHFPASDIPAQARRLYTINPVRIIPDINYRPVPVTPDLNPVTGRPIDLSFAILRSVSPVHLEYMRNIGMHGTMSISILRGERLWGLIACHHRKPNYVDLDGRQACELVAQVLAWQIGVMEEQAITRQTLKGQAIQRSLINDIEQLHDHRAGLARNSEALLELMGASGLCLHSREGVITIGQTPPGPIIDQLAQLAGRSGGSELFQTDRLSTIIPEAGAFAEVASGVLAVPLSRTPPRRVMLWFRPEVAQTVYWAGNPDKSGRLRPRTSFAAWTEQTHGRAIAWQPHEVAAAVEIRDLIIDVIL 503
                                    22        32        42        52        62        72        82||      96|      109       119 ||    135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455|      470       480       490       500   
                                                                                                 83|      96|                  121|                                                                                                                                                                                                                                                                                                                                    455|                                          
                                                                                                  88      100                   128                                                                                                                                                                                                                                                                                                                                     461                                          


Chain B from PDB  Type:PROTEIN  Length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......ee....eeeeee...eeeeee....................hhhhhhhhhh..eee.......eeeeeeee..eeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee......................hhhhhhhhhhh..eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh.hhhhhh......eeeee....eeeee.......hhhhhhhhhh......eee......hhhhhhhhhhhheeeeee........eeeeee....eeeeee...........eeeeee.......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s21 B  14 TCDDEPIHIPGAIQPHGLLLALAADMTIVAGSDNLPELTIGRSAADVFDSETHNRLTIALAEPPIAVTMRKDAGFVGSWHRHDQLVFLELEPPFFRRTNSAIRRLQAAETLESACAAAAQEVREITGFDRVMIYRFASDFSGEVIAEDRCAEVESYLGLHFPASDIPAQARRLYTINPVRIIPDINYRPVPVTPDLNPVTGRPIDLSFAILRSVSPVHLEYMRNIGMHGTMSISILRGERLWGLIACHHRKPNYVDLDGRQACELVAQVLAWQIGVMEEQAITRQTLKGQAIQRSLINDIEQLHDHRAGLARNSEALLELMGASGLCLHSREGVITIGQTPPGPIIDQLAQLAGRSGGSELFQTDRLSTIIPEAGAFAEVASGVLAVPLSRTPPRRVMLWFRPEVAQTVYWAGNPDKSRTSFAAWTEQTHGRAIAWQPHEVAAAVEIRDLIIDVI 502
                                    23        33        43        60        70        80  ||  ||98       108       118  ||   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       467       477       487       497     
                                                                 52|                     83| 93|                      121|                                                                                                                                                                                                                                                                                                                                 455|                                    
                                                                  60                      90  96                       131                                                                                                                                                                                                                                                                                                                                  466
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4S21)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S21)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S21)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:89 - Pro A:90   [ RasMol ]  
    Gly A:450 - Asn A:451   [ RasMol ]  
    Lys B:325 - Gly B:326   [ RasMol ]  
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    Thr A:230 - Pro A:231   [ RasMol ]  
    Thr B:230 - Pro B:231   [ RasMol ]  
    Thr B:429 - Pro B:430   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q6N5G3_RHOPA | Q6N5G3: 4e04 4r6l

(-) Related Entries Specified in the PDB File

4r6l CRYSTAL STRUCTURE OF THE PHOTOSENSORY CORE MODULE OF BACTERIOPHYTOCHROME RPBPHP2 FROM R. PALUSTRIS WITH AN UNCLEAVED C-TERMINAL HIS-TAG
4r70 CRYSTAL STRUCTURE OF THE PHOTOSENSORY CORE MODULE OF BACTERIOPHYTOCHROME RPBPHP3 FROM R. PALUSTRIS