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(-) Description

Title :  CYTOCHROME F FROM THE B6F COMPLEX OF PHORMIDIUM LAMINOSUM
 
Authors :  C. J. Carrell, B. G. Schlarb, C. J. Howe, D. S. Bendall, W. A. Cramer, J. L.
Date :  07 Apr 99  (Deposition) - 11 Aug 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  M
Biol. Unit 1:  M  (1x)
Biol. Unit 2:  M  (6x)
Biol. Unit 3:  M  (2x)
Keywords :  Electron Transfer Protein, Complex Subunit, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Carrell, B. G. Schlarb, D. S. Bendall, C. J. Howe, W. A. Cramer, J. L. Smith
Structure Of The Soluble Domain Of Cytochrome F From The Cyanobacterium Phormidium Laminosum.
Biochemistry V. 38 9590 1999
PubMed-ID: 10423236  |  Reference-DOI: 10.1021/BI9903190
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CYTOCHROME F)
    Cellular Location: MEMBRANE-CYTOPLASM INTERFACE
    Chains: M
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Plasmid: PUC19CF
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE EXTRINSIC FRAGMENT
    Gene: PETA
    Organism Scientific: PHORMIDIUM LAMINOSUM
    Organism Taxid: 32059
    Other Details: THIOETHER LINK BETWEEN CYS 21 AND HEME 254;
COORDINATION OF HEME IRON BY HIS 25 AND N-TERMINAL AMINO GROUP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : M
Biological Unit 1 (1x): M
Biological Unit 2 (6x): M
Biological Unit 3 (2x): M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP M:54 , HIS M:55 , GLU M:125 , HOH M:260BINDING SITE FOR RESIDUE ZN M 256
2AC2SOFTWAREHIS M:150 , GLU M:198 , ASP M:199 , HOH M:274BINDING SITE FOR RESIDUE ZN M 257
3AC3SOFTWARETYR M:1 , TRP M:4 , ALA M:5 , CYS M:21 , CYS M:24 , HIS M:25 , GLN M:59 , LEU M:69 , ASN M:70 , VAL M:71 , GLY M:72 , ASN M:154 , GLY M:156 , ARG M:157 , GLY M:158 , ILE M:160 , TYR M:161 , PRO M:162 , HOH M:262 , HOH M:264 , HOH M:266BINDING SITE FOR RESIDUE HEM M 254

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CI3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly M:117 -Pro M:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CI3)

(-) Exons   (0, 0)

(no "Exon" information available for 1CI3)

(-) 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 M from PDB  Type:PROTEIN  Length:249
 aligned with CYF_PHOLA | P95522 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:249
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285         
            CYF_PHOLA    46 YPFWAQQNYANPREATGRIVCANCHLAAKPAEIEVPQAVLPDSVFKAVVKIPYDHSVQQVQADGSKGPLNVGAVLMLPEGFTIAPEDRIPEEMKEEVGPSYLFQPYADDKQNIVLVGPLPGDQYEEIVFPVLSPNPATNKSVAFGKYSIHLGANRGRGQIYPTGEKSNNAVYNASAAGVITAIAKADDGSAEVKIRTEDGTTIVDKIPAGPELIVSEGEEVAAGAALTNNPNVGGFGQKDTEIVLQSPN 294
               SCOP domains d1ci3m1 M:1-169,M:232-249 Cytochrome f, large domain                                                                                                                     d1ci3m2 M:170-231 Cytochrome f, small domain                  d1ci3m1            SCOP domains
               CATH domains 1ci3M01 M:1-171,M:230-248  [code=2.60.40.830, no name defined]                                                                                                             1ci3M02 M:172-229  [code=2.40.50.100, no name defined]    1ci3M01            - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...........hhhh........eee...................................................hhh..hhhhhh...hhh................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ci3 M   1 YPFWAQQNYANPREATGRIVCANCHLAAKPAEIEVPQAVLPDSVFKAVVKIPYDHSVQQVQADGSKGPLNVGAVLMLPEGFTIAPEDRIPEEMKEEVGPSYLFQPYADDKQNIVLVGPLPGDEYEEIVFPVLSPNPATNKSVAFGKYSIHLGANRGRGQIYPTGEKSNNAVYNASAAGVITAIAKADDGSAEVKIRTEDGTTIVDKIPAGPELIVSEGEEVAAGAALTNNPNVGGFGQKDTEIVLQSPN 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CI3)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain M   (CYF_PHOLA | P95522)
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0031361    integral component of thylakoid membrane    The component of the thylakoid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0042651    thylakoid membrane    The pigmented membrane of any thylakoid.

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