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(-) Description

Title :  CRYSTALLIZATION AND STRUCTURAL ANALYSIS OF CYTOCHROME C6 FROM THE DIATOM PHAEODACTYLUM TRICORNUTUM AT 1.5 A RESOLUTION
 
Authors :  H. Akazaki, F. Kawai, M. Hosokawa, T. Hama, T. Hirano, B. -K. Lim, N. Sakurai, W. Hakamata, S. -Y. Park, T. Nishio, T. Oku
Date :  01 Jul 08  (Deposition) - 17 Mar 09  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport, Cytochrome C6, Crystal Structure, Phaeodactylum Tricornutum, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Akazaki, F. Kawai, M. Hosokawa, T. Hama, H. Chida, T. Hirano, B. -K. Lim, N. Sakurai, W. Hakamata, S. -Y. Park, T. Nishio, T. Oku
Crystallization And Structural Analysis Of Cytochrome C(6) From The Diatom Phaeodactylum Tricornutum At 1. 5 A Resolution
Biosci. Biotechnol. Biochem. V. 73 189 2009
PubMed-ID: 19129656
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C6
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PET J
    Organism Scientific: PHAEODACTYLUM TRICORNUTUM
    Organism Taxid: 2850

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:114 , HOH A:147 , HOH A:177 , HOH A:182 , HOH A:192 , HOH A:246BINDING SITE FOR RESIDUE MG A 134
2AC2SOFTWAREASN A:58 , CYS A:59 , CYS A:62 , HIS A:63 , ASN A:68 , ILE A:70 , LYS A:74 , THR A:75 , LEU A:76 , ALA A:80 , TYR A:84 , LEU A:85 , GLN A:97 , LYS A:102 , ASN A:103 , MET A:105 , PHE A:108 , HOH A:154 , HOH A:170 , HOH A:207BINDING SITE FOR RESIDUE HEM A 146

(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:87
 aligned with Q8GTB5_PHATR | Q8GTB5 from UniProtKB/TrEMBL  Length:133

    Alignment length:87
                                    55        65        75        85        95       105       115       125       
         Q8GTB5_PHATR    46 GDVGAGEQIFNANCAACHAGGQNVIMPEKTLEKEALDQYLAGGRTEKSIISQVTGGKNAMPAFGGRLSDEEIANVAAYVLASAEAGW 132
               SCOP domains d3dmia_ A: automated matches                                                            SCOP domains
               CATH domains 3dmiA00 A:46-132 Cytochrome c                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3dmi A  46 GDVGAGEQIFNANCAACHAGGQNVIMPEKTLEKEALDQYLAGGRTEKSIISQVTGGKNAMPAFGGRLSDEEIANVAAYVLASAEAGW 132
                                    55        65        75        85        95       105       115       125
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8GTB5_PHATR | Q8GTB5)
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.

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