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(-) Description

Title :  STRUCTURE OF THE PFR FORM OF A CANONICAL PHYTOCHROME
 
Authors :  E. S. Burgie, R. D. Vierstra
Date :  20 Jun 15  (Deposition) - 17 Feb 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.31
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Photosensor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Burgie, J. Zhang, R. D. Vierstra
Crystal Structure Of Deinococcus Phytochrome In The Photoactivated State Reveals A Cascade Of Structural Rearrangements During Photoconversion.
Structure V. 24 448 2016
PubMed-ID: 26853942  |  Reference-DOI: 10.1016/J.STR.2016.01.001

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME
    Chains: A, B, C, D
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-502
    Gene: BPHP, DR_A0050
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
    Synonym: PHYTOCHROME-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BGC1Ligand/IonBETA-D-GLUCOSE
3BLA4Ligand/IonBILIVERDINE IX ALPHA
4EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BGC-1Ligand/IonBETA-D-GLUCOSE
3BLA2Ligand/IonBILIVERDINE IX ALPHA
4EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2BGC1Ligand/IonBETA-D-GLUCOSE
3BLA2Ligand/IonBILIVERDINE IX ALPHA
4EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , TYR A:176 , PHE A:198 , HIS A:201 , PHE A:203 , ASP A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:222 , ARG A:254 , THR A:256 , SER A:257 , HIS A:260 , TYR A:263 , LEU A:264 , MET A:267 , SER A:272 , ALA A:288 , HIS A:290 , PRO A:465 , ACT A:603 , HOH A:706binding site for residue BLA A 601
2AC2SOFTWAREALA A:96 , GLU A:306 , ARG A:310binding site for residue EDO A 602
3AC3SOFTWARETYR A:216 , THR A:224 , HIS A:260 , SER A:272 , SER A:274 , BLA A:601binding site for residue ACT A 603
4AC4SOFTWAREASN A:243 , ARG C:375 , TRP C:376 , ASP C:389binding site for residue BGC C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C5K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:235 -Pro A:236
2Asp B:235 -Pro B:236
3Asp C:235 -Pro C:236
4Asp D:235 -Pro D:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C5K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C5K)

(-) Exons   (0, 0)

(no "Exon" information available for 5C5K)

(-) 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:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..................ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh........eeeeeeee...eeeeeeeeee..eeeeeeee.........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhh....eeeeee.......eeeeee...............hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c5k A   7 PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEAWDSTGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVAWGGKDDLGPRHSWDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGAL 502
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446      |462       472       482       492       502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        453|                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         460                                          


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.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh........eeeeeeee...eeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.......eeeeee.......eeeeee.............hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c5k B   7 PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEAWDSTGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVAWKDDLGPRHSWDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGAL 502
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       348       358       368       378       388       398       408       418       428       438       448  ||   466       476       486       496      
                                                                                                                                                                                                                                                                                                                                                                            345|                                                                                                    451|                                          
                                                                                                                                                                                                                                                                                                                                                                             348                                                                                                     460                                          


Chain C from PDB  Type:PROTEIN  Length:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..................ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh........eeeeeee...eeeeeeeee..eeeeeeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh...eeeeee..eeeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh......eeeeee.......eeeeee........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c5k C   7 PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWAGHLSLTVHRVGELLILEFEPTEAHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVLGPRHSWDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALE 503
                                    16        26        36        46        56        66        76        86        96       108       118       128  ||   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    || 467       477       487       497      
                                                                                                                            105|                    131|                                                                                                                                                                                                                                                                                                                    449|                                        
                                                                                                                             108                     138                                                                                                                                                                                                                                                                                                                     463                                        


Chain D from PDB  Type:PROTEIN  Length:474
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh..................ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh........eeeeeee...eeeeeeeee..eeeeeeee...hhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh......eeeeee.......eeeeee..........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c5k D   7 PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWAGHLSLTVHRVGELLILEFEPTEALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVAWGPRHSWDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGAL 502
                                    16        26        36        46        56        66        76        86        96       108       118       128 ||    146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446    || 468       478       488       498    
                                                                                                                            105|                   130|                                                                                                                                                                                                                                                                                                                     451|                                      
                                                                                                                             108                    139                                                                                                                                                                                                                                                                                                                      464
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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 5C5K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C5K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C5K)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        BPHY_DEIRA | Q9RZA4: 1ztu 2o9b 2o9c 3s7n 3s7o 3s7p 3s7q 4cqh 4ijg 4o01 4o0p 4o8g 4q0h 4q0i 4q0j 4y3i 4y5f 4z1w 4zrr 5ajg 5k5b 5l8m 5lbr 5mg0 5mg1

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