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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION
 
Authors :  M. Archer, L. Banci, E. Dikaya, M. J. Romao
Date :  24 Jun 97  (Deposition) - 21 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Electron Transport, Heme Protein, Cytochrome C' (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Archer, L. Banci, E. Dikaya, M. J. Romao
Crystal Structure Of Cytochrome C' From Rhodocyclus Gelatinosus And Comparison With Other Cytochromes C'
J. Biol. Inorg. Chem. V. 2 611 1997
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A, B
    Organism Scientific: RUBRIVIVAX GELATINOSUS
    Organism Taxid: 28068

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , PHE A:16 , THR A:17 , THR A:69 , GLU A:70 , PHE A:82 , ALA A:86 , PHE A:89 , ALA A:118 , CYS A:119 , CYS A:122 , HIS A:123 , LYS A:127 , HOH A:231 , HOH A:244BINDING SITE FOR RESIDUE HEM A 130
2AC2SOFTWAREARG B:12 , GLN B:13 , PHE B:16 , THR B:17 , THR B:69 , GLU B:70 , ALA B:86 , PHE B:89 , CYS B:119 , CYS B:122 , HIS B:123 , PHE B:126 , LYS B:127 , HOH B:214BINDING SITE FOR RESIDUE HEM B 130

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JAF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JAF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JAF)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_RUBGE7-128
 		  2A:7-128
B:7-128
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_RUBGE7-128
 		  4A:7-128
B:7-128

(-) Exons   (0, 0)

(no "Exon" information available for 1JAF)

(-) 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:128
 aligned with CYCP_RUBGE | P00142 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           CYCP_RUBGE     1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKE 128
               SCOP domains d1jafa_ A: Cytochrome c'                                                                                                         SCOP domains
               CATH domains 1jafA00 A:1-128  [code=1.20.120.10, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: A:7-128 UniProt: 7-128                                                                                        PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jaf A   1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKE 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with CYCP_RUBGE | P00142 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           CYCP_RUBGE     1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKE 128
               SCOP domains d1jafb_ B: Cytochrome c'                                                                                                         SCOP domains
               CATH domains 1jafB00 B:1-128  [code=1.20.120.10, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: B:7-128 UniProt: 7-128                                                                                        PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jaf B   1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKE 128
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JAF)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYCP_RUBGE | P00142)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYCP_RUBGE | P00142: 2j8w 2j9b

(-) Related Entries Specified in the PDB File

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