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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOCHROME C' FROM THERMOCHROMATIUM TEPIDUM
 
Authors :  Y. Hirano, Y. Kimura, H. Suzuki, K. Miki, Z. -Y. Wang
Date :  09 Apr 12  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C-Type Cytpchrome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hirano, Y. Kimura, H. Suzuki, K. Miki, Z. -Y. Wang
Structure Analysis And Comparative Characterization Of The Cytochrome C' And Flavocytochrome C From Thermophilic Purpl Photosynthetic Bacterium Thermochromatium Tepidum
Biochemistry V. 51 6556 2012
PubMed-ID: 22827326  |  Reference-DOI: 10.1021/BI3005522

(-) Compounds

Molecule 1 - CYTOCHROME C'
    Chains: A, B
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1CD9Ligand/IonCADMIUM ION
2CL1Ligand/IonCHLORIDE ION
3HEC2Ligand/IonHEME C
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:12 , GLN A:13 , TYR A:16 , MET A:19 , TYR A:58 , THR A:71 , ARG A:72 , LEU A:77 , VAL A:84 , ALA A:88 , CYS A:121 , CYS A:124 , HIS A:125 , ARG A:129 , HOH A:302 , HOH A:390 , HOH A:471 , GLU B:106 , ASN B:108 , CD B:202 , HOH B:302 , HOH B:380 , HOH B:424 , HOH B:518 , HOH B:529BINDING SITE FOR RESIDUE HEC A 200
02AC2SOFTWAREGLU A:82 , CL A:206 , GLU B:76BINDING SITE FOR RESIDUE CD A 201
03AC3SOFTWAREASP A:131 , HOH A:319 , HOH A:320 , HOH A:325 , HOH A:371 , HOH A:501BINDING SITE FOR RESIDUE CD A 202
04AC4SOFTWAREASP A:116 , HOH A:337 , HOH A:402 , HOH A:502BINDING SITE FOR RESIDUE CD A 203
05AC5SOFTWAREGLU A:76 , HOH A:382 , HOH A:457BINDING SITE FOR RESIDUE CD A 204
06AC6SOFTWAREGLU A:7 , HOH A:486 , HOH A:499BINDING SITE FOR RESIDUE CD A 205
07AC7SOFTWARECD A:201 , HOH A:460 , PRO B:75 , GLU B:76BINDING SITE FOR RESIDUE CL A 206
08AC8SOFTWAREGLU A:82 , ASP A:83 , ARG A:89 , HOH A:379 , HOH A:436 , GLN B:79 , HOH B:349BINDING SITE FOR RESIDUE PEG A 207
09AC9SOFTWARETYR A:58 , GLY A:59 , PRO A:60 , GLY A:61 , ASP A:63 , LYS A:64 , PHE A:78 , LEU A:81 , HOH A:514 , HOH A:515BINDING SITE FOR RESIDUE PG4 A 208
10BC1SOFTWAREARG B:12 , GLN B:13 , TYR B:16 , ALA B:17 , TYR B:58 , THR B:71 , ARG B:72 , LEU B:77 , VAL B:84 , ALA B:88 , LEU B:91 , CYS B:121 , CYS B:124 , HIS B:125 , ARG B:129 , HOH B:304BINDING SITE FOR RESIDUE HEC B 201
11BC2SOFTWAREHEC A:200 , ASN B:108 , HOH B:302 , HOH B:311 , HOH B:424 , HOH B:518BINDING SITE FOR RESIDUE CD B 202
12BC3SOFTWAREASP B:37 , HOH B:435 , HOH B:523 , HOH B:542BINDING SITE FOR RESIDUE CD B 203
13BC4SOFTWAREASP B:131 , HOH B:344 , HOH B:378 , HOH B:379 , HOH B:473 , HOH B:537BINDING SITE FOR RESIDUE CD B 204
14BC5SOFTWAREASP B:63 , HOH B:437 , HOH B:474BINDING SITE FOR RESIDUE CD B 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VRC)

(-) Exons   (0, 0)

(no "Exon" information available for 3VRC)

(-) 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:130
 aligned with C7G528_THETI | C7G528 from UniProtKB/TrEMBL  Length:154

    Alignment length:130
                                    34        44        54        64        74        84        94       104       114       124       134       144       154
         C7G528_THETI    25 DLSPEEQIETRQAGYAFMAWNMGKIKANLEGEYNADQVRAAANVVAAIANSGMGALYGPGTDKNVGAVKTRAKPELFQNLEDVGKLARDLGTAANALAAAAATGEANAVKSAFADVGAACKACHQKYRAD 154
               SCOP domains d3vrca_ A: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrc A   2 DLSPEEQIETRQAGYAFMAWNMGKIKANLEGEYNADQVRAAANVVAAIANSGMGALYGPGTDKNVGAVKTRAKPELFQNLEDVGKLARDLGTAANALAAAAATGEANAVKSAFADVGAACKACHQKYRAD 131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with C7G528_THETI | C7G528 from UniProtKB/TrEMBL  Length:154

    Alignment length:131
                                    33        43        53        63        73        83        93       103       113       123       133       143       153 
         C7G528_THETI    24 ADLSPEEQIETRQAGYAFMAWNMGKIKANLEGEYNADQVRAAANVVAAIANSGMGALYGPGTDKNVGAVKTRAKPELFQNLEDVGKLARDLGTAANALAAAAATGEANAVKSAFADVGAACKACHQKYRAD 154
               SCOP domains d3vrcb_ B: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrc B   1 ADLSPEEQIETRQAGYAFMAWNMGKIKANLEGEYNADQVRAAANVVAAIANSGMGALYGPGTDKNVGAVKTRAKPELFQNLEDVGKLARDLGTAANALAAAAATGEANAVKSAFADVGAACKACHQKYRAD 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VRC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (C7G528_THETI | C7G528)
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.
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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3vrd