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(-) Description

Title :  CRYSTAL STRUCTURE OF LOW-REDOX-POTENTIAL CYTOCHROM C6 FROM BROWN ALGA HIZIKIA FUSIFORMIS AT 1.6 A RESOLUTION
 
Authors :  H. Akazaki, F. Kawai, H. Chida, Y. Matsumoto, I. Sirasaki, H. Nakade, M. Hirayama, K. Hosikawa, K. Suruga, T. Satoh, S. Yamada, S. Unzai, W. Hakamata, T. Nishio, S. -Y. Park, T. Oku
Date :  26 Oct 07  (Deposition) - 30 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,C,E,G,I,K
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  G  (1x)
Biol. Unit 5:  I  (1x)
Biol. Unit 6:  K  (1x)
Biol. Unit 7:  A,C,E,G,I,K  (1x)
Keywords :  Electron Transport, Cytochrome C6, Redox Potential, Brown Alga, Heme, Iron, Metal-Binding, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Akazaki, F. Kawai, H. Chida, Y. Matsumoto, M. Hirayama, K. Hoshikawa, S. Unzai, W. Hakamata, T. Nishio, S. -Y. Park, T. Oku
Cloning, Expression And Purification Of Cytochrome C(6) From The Brown Alga Hizikia Fusiformis And Complete X-Ray Diffraction Analysis Of The Structure
Acta Crystallogr. , Sect. F V. 64 674 2008
PubMed-ID: 18678931  |  Reference-DOI: 10.1107/S1744309108017752
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C6
    Chains: A, C, E, G, I, K
    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: PETJ
    Organism Scientific: HIZIKIA FUSIFORMIS
    Organism Taxid: 74103
    Strain: BROWN ALGA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ACEGIK
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  C    
Biological Unit 3 (1x):   E   
Biological Unit 4 (1x):    G  
Biological Unit 5 (1x):     I 
Biological Unit 6 (1x):      K
Biological Unit 7 (1x): ACEGIK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION
Biological Unit 7 (2, 10)
No.NameCountTypeFull Name
1HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER E:67 , VAL E:68 , HOH E:124 , SER G:90 , ASP G:91 , HOH G:313 , HOH G:374BINDING SITE FOR RESIDUE SO4 G 1
02AC2SOFTWAREGLY A:87 , ARG A:88 , HOH A:167 , HOH A:206 , HOH A:216 , HOH A:223 , HOH A:225 , GLY C:87 , ARG C:88 , GLY E:87 , ARG E:88BINDING SITE FOR RESIDUE SO4 A 2
03AC3SOFTWAREGLY A:44 , TRP A:109 , MET I:50 , PRO I:51 , GLU I:52 , HOH I:113 , HOH I:114 , HOH I:116BINDING SITE FOR RESIDUE SO4 I 3
04AC4SOFTWAREGLY C:44 , TRP C:109 , HOH C:149 , MET K:50 , PRO K:51 , GLU K:52 , HOH K:119BINDING SITE FOR RESIDUE SO4 K 4
05AC5SOFTWAREASN A:37 , CYS A:38 , CYS A:41 , HIS A:42 , ASN A:47 , LYS A:53 , THR A:54 , LEU A:55 , ALA A:59 , ASN A:63 , GLN A:74 , VAL A:75 , LYS A:79 , ASN A:80 , MET A:82 , PHE A:85 , HOH A:138 , HOH A:157 , HOH A:194 , HOH A:198 , ALA C:36BINDING SITE FOR RESIDUE HEM A 111
06AC6SOFTWAREASN C:37 , CYS C:38 , CYS C:41 , HIS C:42 , ASN C:47 , LYS C:53 , THR C:54 , LEU C:55 , ALA C:59 , ASN C:63 , GLN C:74 , VAL C:75 , LYS C:79 , ASN C:80 , MET C:82 , PHE C:85 , HOH C:120 , HOH C:134 , ALA E:36BINDING SITE FOR RESIDUE HEM C 111
07AC7SOFTWAREALA A:36 , ASN E:37 , CYS E:38 , CYS E:41 , HIS E:42 , ASN E:47 , LYS E:53 , THR E:54 , LEU E:55 , ALA E:59 , ASN E:63 , GLN E:74 , VAL E:75 , LYS E:79 , ASN E:80 , MET E:82 , PHE E:85 , HOH E:125 , HOH E:133 , HOH E:162BINDING SITE FOR RESIDUE HEM E 111
08AC8SOFTWAREASN G:37 , CYS G:38 , CYS G:41 , HIS G:42 , ASN G:47 , LYS G:53 , THR G:54 , LEU G:55 , ASN G:63 , MET G:65 , GLN G:74 , VAL G:75 , LYS G:79 , ASN G:80 , MET G:82 , PHE G:85 , HOH G:301 , HOH G:307BINDING SITE FOR RESIDUE HEM G 111
09AC9SOFTWAREASN I:37 , CYS I:38 , CYS I:41 , HIS I:42 , ASN I:47 , MET I:50 , LYS I:53 , THR I:54 , LEU I:55 , ALA I:59 , ASN I:63 , MET I:65 , GLN I:74 , LYS I:79 , ASN I:80 , MET I:82 , PHE I:85 , HOH I:120 , HOH I:126BINDING SITE FOR RESIDUE HEM I 111
10BC1SOFTWAREASN K:37 , CYS K:38 , CYS K:41 , HIS K:42 , ASN K:47 , ILE K:49 , MET K:50 , LYS K:53 , THR K:54 , LEU K:55 , ALA K:59 , ASN K:63 , GLN K:74 , VAL K:75 , LYS K:79 , ASN K:80 , MET K:82 , PHE K:85 , HOH K:127 , HOH K:133 , HOH K:177BINDING SITE FOR RESIDUE HEM K 111

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZBO)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZBO)

(-) 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:86
 aligned with Q76FN8_SARFS | Q76FN8 from UniProtKB/TrEMBL  Length:110

    Alignment length:86
                                    34        44        54        64        74        84        94       104      
         Q76FN8_SARFS    25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
               SCOP domains d2zboa_ A: automated matches                                                           SCOP domains
               CATH domains 2zboA00 A:25-110 Cytochrome c                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zbo A  25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
                                    34        44        54        64        74        84        94       104      


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with Q76FN8_SARFS | Q76FN8 from UniProtKB/TrEMBL  Length:110

    Alignment length:86
                                    34        44        54        64        74        84        94       104      
         Q76FN8_SARFS    25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
               SCOP domains d2zboc_ C: automated matches                                                           SCOP domains
               CATH domains 2zboC00 C:25-110 Cytochrome c                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zbo C  25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
                                    34        44        54        64        74        84        94       104      


Chain E from PDB  Type:PROTEIN  Length:86
 aligned with Q76FN8_SARFS | Q76FN8 from UniProtKB/TrEMBL  Length:110

    Alignment length:86
                                    34        44        54        64        74        84        94       104      
         Q76FN8_SARFS    25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
               SCOP domains d2zboe_ E: automated matches                                                           SCOP domains
               CATH domains 2zboE00 E:25-110 Cytochrome c                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zbo E  25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
                                    34        44        54        64        74        84        94       104      


Chain G from PDB  Type:PROTEIN  Length:86
 aligned with Q76FN8_SARFS | Q76FN8 from UniProtKB/TrEMBL  Length:110

    Alignment length:86
                                    34        44        54        64        74        84        94       104      
         Q76FN8_SARFS    25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
               SCOP domains d2zbog_ G: automated matches                                                           SCOP domains
               CATH domains 2zboG00 G:25-110 Cytochrome c                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zbo G  25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
                                    34        44        54        64        74        84        94       104      


Chain I from PDB  Type:PROTEIN  Length:86
 aligned with Q76FN8_SARFS | Q76FN8 from UniProtKB/TrEMBL  Length:110

    Alignment length:86
                                    34        44        54        64        74        84        94       104      
         Q76FN8_SARFS    25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
               SCOP domains d2zboi_ I: automated matches                                                           SCOP domains
               CATH domains 2zboI00 I:25-110 Cytochrome c                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zbo I  25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
                                    34        44        54        64        74        84        94       104      


Chain K from PDB  Type:PROTEIN  Length:86
 aligned with Q76FN8_SARFS | Q76FN8 from UniProtKB/TrEMBL  Length:110

    Alignment length:86
                                    34        44        54        64        74        84        94       104      
         Q76FN8_SARFS    25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
               SCOP domains d2zbok_ K: automated matches                                                           SCOP domains
               CATH domains 2zboK00 K:25-110 Cytochrome c                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zbo K  25 ADINHGENVFTANCSACHAGGNNVIMPEKTLQKDALSTNQMNSVGAITYQVTNGKNAMPAFGGRLSDDDIEDVASFVLSQSEKSWN 110
                                    34        44        54        64        74        84        94       104
   Legend:   → Mismatch (orange background)
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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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G,I,K   (Q76FN8_SARFS | Q76FN8)
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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