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(-) Description

Title :  X-RAY STRUCTURE OF THE CYTOCHROME C-554 FROM CHLOROBACULUM TEPIDUM
 
Authors :  M. Unno, L. J. Yu, Z. Y. Wang-Otomo
Date :  04 Feb 13  (Deposition) - 02 Oct 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytocrome C, Electron Transfer, Cytochrome Cz, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Yu, M. Unno, Y. Kimura, K. Yanagimoto, H. Oh-Oka, Z. Y. Wang-Otomo
Structure Analysis And Characterization Of The Cytochrome C-554 From Thermophilic Green Sulfur Photosynthetic Bacterium Chlorobaculum Tepidum
Photosynth. Res. V. 118 249 2013
PubMed-ID: 24052268  |  Reference-DOI: 10.1007/S11120-013-9922-2

(-) Compounds

Molecule 1 - CYTOCHROME C-555
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-108
    Gene: CT0075
    Mutation: YES
    Organism Scientific: CHLOROBIUM TEPIDUM
    Organism Taxid: 194439
    Strain: ATCC 49652 / DSM 12025 / TLS
    Synonym: CYTOCHROME C555

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1HEB2Ligand/IonHEME B/C
2IPA7Ligand/IonISOPROPYL ALCOHOL
3NA1Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1HEB1Ligand/IonHEME B/C
2IPA4Ligand/IonISOPROPYL ALCOHOL
3NA-1Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1HEB1Ligand/IonHEME B/C
2IPA3Ligand/IonISOPROPYL ALCOHOL
3NA-1Ligand/IonSODIUM ION
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:43 , MET A:44 , ASN A:45 , NA A:106 , HOH A:246 , HOH A:311 , HOH A:322 , HOH A:414 , HOH A:418 , GLY B:43 , MET B:44BINDING SITE FOR RESIDUE SO4 A 101
02AC2SOFTWARESER A:1 , HOH A:310 , HOH A:314 , THR B:2BINDING SITE FOR RESIDUE IPA A 102
03AC3SOFTWAREGLN A:86BINDING SITE FOR RESIDUE IPA A 103
04AC4SOFTWAREMET A:61 , HOH A:313 , HOH A:331 , HOH A:346 , LYS B:59BINDING SITE FOR RESIDUE IPA A 104
05AC5SOFTWAREALA A:69 , LYS A:70 , LEU A:71 , ILE B:52 , LYS B:53BINDING SITE FOR RESIDUE IPA A 105
06AC6SOFTWARESO4 A:101 , HOH A:271 , HOH A:359 , MET B:44BINDING SITE FOR RESIDUE NA A 106
07AC7SOFTWARESER A:15 , CYS A:16 , CYS A:19 , HIS A:20 , ALA A:27 , PRO A:28 , ARG A:39 , GLN A:42 , LEU A:47 , LYS A:50 , SER A:51 , TYR A:55 , GLY A:57 , THR A:58 , LYS A:59 , GLY A:60 , MET A:61 , MET A:62 , GLY A:66 , VAL A:80 , MET A:83 , HOH A:403BINDING SITE FOR RESIDUE HEB A 107
08AC8SOFTWARELYS A:59 , HOH A:224 , THR B:22 , LYS B:29BINDING SITE FOR RESIDUE IPA B 101
09AC9SOFTWAREALA A:34 , GLY B:31 , GLN B:86BINDING SITE FOR RESIDUE IPA B 102
10BC1SOFTWAREHOH A:276 , HOH A:416 , THR B:18 , CYS B:19 , MET B:25BINDING SITE FOR RESIDUE IPA B 103
11BC2SOFTWAREHOH A:384 , SER B:15 , CYS B:16 , CYS B:19 , HIS B:20 , GLY B:26 , ALA B:27 , PRO B:28 , TRP B:36 , ARG B:39 , GLN B:42 , LEU B:47 , LYS B:50 , SER B:51 , TYR B:55 , GLY B:57 , THR B:58 , LYS B:59 , GLY B:60 , MET B:61 , MET B:62 , LYS B:65 , GLY B:66 , MET B:83BINDING SITE FOR RESIDUE HEB B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J20)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J20)

(-) Exons   (0, 0)

(no "Exon" information available for 4J20)

(-) 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:88
                                                                                                                       
               SCOP domains d4j20a_ A: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhh.hhhhhhhhhhhhee....eehhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4j20 A  1 STYDAAAGKATYDASCATCHKTGMMGAPKVGDKAAWAPRIAQGMNTLVSKSIKGYKGTKGMMPAKGGNAKLTDAQVGNAVAYMVGQSK 88
                                    10        20        30        40        50        60        70        80        


Chain B from PDB  Type:PROTEIN  Length:88
                                                                                                                       
               SCOP domains d4j20b_ B: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhee....eehhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  4j20 B  1 STYDAAAGKATYDASCATCHKTGMMGAPKVGDKAAWAPRIAQGMNTLVSKSIKGYKGTKGMMPAKGGNAKLTDAQVGNAVAYMVGQSK 88
                                    10        20        30        40        50        60        70        80
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J20)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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