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(-) Description

Title :  STRUCTURE OF REDUCED CYTOCHROME C6 FROM SYNECHOCOCCUS SP. PCC 7002
 
Authors :  W. Bialek, S. Krzywda, M. Jaskolski, A. Szczepaniak
Date :  10 Jul 08  (Deposition) - 14 Jul 09  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.23
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cytochrome, Photosynthesis, Cyanobacteria, Electron Transfer, Electron Transport, Heme, Iron, Metal-Binding, Thylakoid, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Bialek, S. Krzywda, M. Jaskolski, A. Szczepaniak
Atomic-Resolution Structure Of Reduced Cyanobacterial Cytochrome C6 With An Unusual Sequence Insertion
Febs J. V. 276 4426 2009
PubMed-ID: 19678839  |  Reference-DOI: 10.1111/J.1742-4658.2009.07150.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C6
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC19
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePETJ
    Organism CommonAGMENELLUM QUADRUPLICATUM
    Organism ScientificSYNECHOCOCCUS SP. PCC 7002
    Organism Taxid32049
    SynonymSOLUBLE CYTOCHROME F, CYTOCHROME C553, CYTOCHROME C-553

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:198 , HOH B:232 , HOH B:233 , ARG C:71BINDING SITE FOR RESIDUE SO4 B 96
2AC2SOFTWAREPRO B:66 , ALA B:67 , HOH B:117 , HOH B:262 , SER C:73 , ASP C:74BINDING SITE FOR RESIDUE SO4 B 95
3AC3SOFTWAREASN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , ASN A:23 , MET A:26 , LYS A:29 , THR A:30 , LEU A:31 , TYR A:39 , GLN A:57 , VAL A:58 , GLN A:62 , MET A:65 , PRO A:66 , PHE A:68 , ILE A:84 , HOH A:103 , HOH A:105 , HOH A:106BINDING SITE FOR RESIDUE HEM A 94
4AC4SOFTWAREASN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , ASN B:23 , VAL B:25 , MET B:26 , LYS B:29 , THR B:30 , LEU B:31 , LEU B:36 , TYR B:39 , GLN B:57 , VAL B:58 , GLN B:62 , MET B:65 , PHE B:68 , ILE B:84 , HOH B:104 , HOH B:116 , HOH B:224 , HOH B:279 , HOH B:283BINDING SITE FOR RESIDUE HEM B 94
5AC5SOFTWAREASN C:13 , CYS C:14 , CYS C:17 , HIS C:18 , ASN C:23 , MET C:26 , LYS C:29 , THR C:30 , LEU C:31 , ALA C:35 , TYR C:39 , GLN C:57 , VAL C:58 , GLN C:62 , MET C:65 , PRO C:66 , PHE C:68 , ILE C:84 , HOH C:99 , HOH C:102 , HOH C:112 , HOH C:129BINDING SITE FOR RESIDUE HEM C 94

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DR0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DR0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DR0)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_SYNP225-112
 
 
  3A:1-88
B:1-88
C:1-88
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_SYNP225-112
 
 
  1A:1-88
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_SYNP225-112
 
 
  1-
B:1-88
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC6_SYNP225-112
 
 
  1-
-
C:1-88

(-) Exons   (0, 0)

(no "Exon" information available for 3DR0)

(-) 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:93
 aligned with CYC6_SYNP2 | O30881 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:93
                                    34        44        54        64        74        84        94       104       114   
           CYC6_SYNP2    25 ADAAAGAQVFAANCAACHAGGNNAVMPTKTLKADALKTYLAGYKDGSKSLEEAVAYQVTNGQGAMPAFGGRLSDADIANVAAYIADQAENNKW 117
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dr0A00 A:1-93 Cytochrome c                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:1-88 UniProt: 25-112                                                       ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3dr0 A   1 ADAAAGAQVFAANCAACHAGGNNAVMPTKTLKADALKTYLAGYKDGSKSLEEAVAYQVTNGQGAMPAFGGRLSDADIANVAAYIADQAENNKW  93
                                    10        20        30        40        50        60        70        80        90   

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with CYC6_SYNP2 | O30881 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:93
                                    34        44        54        64        74        84        94       104       114   
           CYC6_SYNP2    25 ADAAAGAQVFAANCAACHAGGNNAVMPTKTLKADALKTYLAGYKDGSKSLEEAVAYQVTNGQGAMPAFGGRLSDADIANVAAYIADQAENNKW 117
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dr0B00 B:1-93 Cytochrome c                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-88 UniProt: 25-112                                                       ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3dr0 B   1 ADAAAGAQVFAANCAACHAGGNNAVMPTKTLKADALKTYLAGYKDGSKSLEEAVAYQVTNGQGAMPAFGGRLSDADIANVAAYIADQAENNKW  93
                                    10        20        30        40        50        60        70        80        90   

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with CYC6_SYNP2 | O30881 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:93
                                    34        44        54        64        74        84        94       104       114   
           CYC6_SYNP2    25 ADAAAGAQVFAANCAACHAGGNNAVMPTKTLKADALKTYLAGYKDGSKSLEEAVAYQVTNGQGAMPAFGGRLSDADIANVAAYIADQAENNKW 117
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dr0C00 C:1-93 Cytochrome c                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: C:1-88 UniProt: 25-112                                                       ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3dr0 C   1 ADAAAGAQVFAANCAACHAGGNNAVMPTKTLKADALKTYLAGYKDGSKSLEEAVAYQVTNGQGAMPAFGGRLSDADIANVAAYIADQAENNKW  93
                                    10        20        30        40        50        60        70        80        90   

   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  (0, 0)

(no "SCOP Domain" information available for 3DR0)

(-) CATH Domains  (1, 3)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DR0)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CYC6_SYNP2 | O30881)
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: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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
cellular component
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0031977    thylakoid lumen    The volume enclosed by a thylakoid membrane.

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        CYC6_SYNP2 | O308811t58 4eic 4eid

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