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(-) Description

Title :  THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT 1.5 A RESOLUTION AND PH 6.3
 
Authors :  S. Benini, S. Ciurli, W. R. Rypniewski, K. S. Wilson
Date :  06 Nov 06  (Deposition) - 04 Dec 07  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heme, Iron, Transport, Metal-Binding, Electron Transfer, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Benini, W. R. Rypniewski, K. S. Wilson, S. Ciurli
High Resolution Crystal Structure Of Rubrivivax Gelatinosus Cytochrome C'.
J. Inorg. Biochem. V. 102 1322 2008
PubMed-ID: 18295896  |  Reference-DOI: 10.1016/J.JINORGBIO.2008.01.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A, B
    Organism Scientific: RHODOCYCLUS GELATINOSUS
    Organism Taxid: 28068
    Other Details: DSMZ
    Strain: DSM 1709

 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
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:12 , GLN A:13 , PHE A:16 , PHE A:59 , THR A:69 , GLU A:70 , PHE A:82 , ALA A:86 , PHE A:89 , CYS A:119 , CYS A:122 , HIS A:123 , LYS A:127 , HOH A:2049 , HOH A:2159 , HOH A:2160 , HOH A:2229 , HOH A:2230 , HOH A:2231BINDING SITE FOR RESIDUE HEM A1128
2AC2SOFTWAREARG B:12 , GLN B:13 , PHE B:16 , THR B:17 , PHE B:59 , THR B:69 , GLU B:70 , PHE B:82 , ALA B:85 , ALA B:86 , PHE B:89 , CYS B:119 , CYS B:122 , HIS B:123 , LYS B:127 , HOH B:2219 , HOH B:2220 , HOH B:2221 , HOH B:2222 , HOH B:2223 , HOH B:2224BINDING SITE FOR RESIDUE HEM B1129

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J9B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J9B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J9B)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCIIPS51009 Cytochrome c class II profile.CYCP_RUBGE7-128
 		  2A:7-127
B:7-128

(-) Exons   (0, 0)

(no "Exon" information available for 2J9B)

(-) 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:127
 aligned with CYCP_RUBGE | P00142 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           CYCP_RUBGE     1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFK 127
               SCOP domains d2j9ba_ A: automated matches                                                                                                    SCOP domains
               CATH domains 2j9bA00 A:1-127  [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:7-127 UniProt: 7-128                                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9b A   1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFK 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


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

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           CYCP_RUBGE     1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKEK 129
               SCOP domains d2j9bb_ B: automated matches                                                                                                      SCOP domains
               CATH domains 2j9bB00 B:1-129  [code=1.20.120.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: B:7-128 UniProt: 7-128                                                                                       - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9b B   1 QFQKPGDAIEYRQSAFTLIANHFGRVAAMAQGKAPFDAKVAAENIALVSTLSKLPLTAFGPGTDKGHGTEAKPAVWSDAAGFKAAADKFAAAVDKLDAAGKTGDFAQIKAAVGETGGACKGCHDKFKEK 129
                                    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)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J9B)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological 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: 1jaf 2j8w

(-) Related Entries Specified in the PDB File

1jaf CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION
2j8w THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT 1.3 A RESOLUTION AND PH 8.0