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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIOPHYTOCHROME RPBPHP3 FROM PHOTOSYNTHETIC BACTERIUM R. PALUSTRIS
 
Authors :  X. Yang, J. Kuk, K. Moffat
Date :  26 Aug 14  (Deposition) - 15 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Pas Fold, Photoreceptor, Response Regulator Rpa3017, 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), PHYB2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PHOTOSENSORY CORE MODULE, UNP RESIDUES 1-521
    Gene: PHYB2, RPA3016
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS CGA009
    Organism Taxid: 258594
    Strain: CGA009

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BLA2Ligand/IonBILIVERDINE IX ALPHA
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BLA2Ligand/IonBILIVERDINE IX ALPHA
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1BLA4Ligand/IonBILIVERDINE IX ALPHA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:28 , ILE A:33 , PHE A:212 , SER A:215 , ASP A:216 , ILE A:217 , PRO A:218 , SER A:221 , TYR A:225 , ARG A:263 , VAL A:265 , SER A:266 , THR A:268 , HIS A:269 , TYR A:272 , ALA A:281 , SER A:283 , SER A:297 , HIS A:299 , PRO A:468 , VAL A:469 , HOH A:1014BINDING SITE FOR RESIDUE BLA A 900
2AC2SOFTWARECYS B:28 , ILE B:33 , VAL B:195 , SER B:215 , ASP B:216 , ILE B:217 , PRO B:218 , SER B:221 , TYR B:225 , ARG B:263 , VAL B:265 , SER B:266 , THR B:268 , HIS B:269 , TYR B:272 , ALA B:281 , MET B:282 , SER B:283 , SER B:297 , HIS B:299 , PRO B:468 , VAL B:469BINDING SITE FOR RESIDUE BLA B 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R70)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asn A:103 -Pro A:104
2Val A:244 -Pro A:245
3Asp B:98 -Pro B:99
4Asn B:103 -Pro B:104
5Val B:244 -Pro B:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R70)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R70)

(-) Exons   (0, 0)

(no "Exon" information available for 4R70)

(-) Sequences/Alignments

Asymmetric 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh......ee....eeeeee....eeeeee.hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.........eeeee......eeeeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhh....eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhh..eeeeee.......eeeeee....eeeee........eee...eeee.......eeeee.......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r70 A  25 LTECDREPIHIPGAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRDESRYTNEFFRSVRVAIRRLQTAADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRDSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSVLRSVSPTHLEYMVNMGMHAAMSISIVRDNRLWGMISCHNLTPRFVSYEVRQACELIAQVLTWQIGVLEEAEIVRHSVRMRAIQNRLLHELGDEQGLTAGLSRVSEEMLALMGASGFALCSFDGVAAFGRTPSDDEIQALASWLSHRESRGIFQTQQLSASFPEAEVYSDIASGLLAVPLGRASTTLMLWFRPEVAQTVTWGGDPHKPVQIGPRGRRLQTRASFEAWREEVRDRSRPWRSHEIVAAEEIRDLVVDVILGRAL 522
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514        


Chain B from PDB  Type:PROTEIN  Length:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.......ee....eeeeee....eeeeee.hhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhh.......eeeee......eeeeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhh...eeee.......eeee.....................hhhhhhhhhhhh..eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee..eeeeee...hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhh..eeeeee.......eeeeee....eeeee..................eeeee.......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r70 B  25 LTECDREPIHIPGAIQPHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGGDPAAINPIRLDVVTPDGERAFNGILHRHDSIVILELEPRYTNEFFRSVRVAIRRLQTAADLPTACWIAASEVRRITGFDRIKVYQFAADWSGQVIAEDRDSGIPSLLDFHFPSSDIPAQSRALYTINPVRIIPDIGYRPSPLVPDINPRLGGPIDLSFSVLRSVSPTHLEYMVNMGMHAAMSISIVRDNRLWGMISCHNLTPRFVSYEVRQACELIAQVLTWQIGVLEEAEIVRHSVRMRAIQNRLLHELGDEQGLTAGLSRVSEEMLALMGASGFALCSFDGVAAFGRTPSDDEIQALASWLSHRESRGIFQTQQLSASFPEAEVYSDIASGLLAVPLGRASTTLMLWFRPEVAQTVTWGGDPHKPVRLQTRASFEAWREEVRDRSRPWRSHEIVAAEEIRDLVVDVILGRA 521
                                    34        44        54        64        74        84        94       104       114       124       134 ||    148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468||     485       495       505       515      
                                                                                                                                         136|                                                                                                                                                                                                                                                                                                                                     469|                                            
                                                                                                                                          141                                                                                                                                                                                                                                                                                                                                      477
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  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 4R70)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R70)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        Q6N5G2_RHOPA | Q6N5G2: 2ool

(-) Related Entries Specified in the PDB File

2ool CRYSTAL STRUCTURE OF A SHORTER CONSTRUCT
4r6l CRYSTAL STRUCTURE OF A CLOSELY RELATED BACTERIOPHYTOCHROME