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(-) Description

Title :  ULTRA-HIGH RESOLUTION STRUCTURE OF P. ABYSSI RUBREDOXIN W4L/R5S/A44S
 
Authors :  H. Boenisch, R. Ladenstein
Date :  16 May 07  (Deposition) - 29 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.86
Chains :  Asym./Biol. Unit :  A
Keywords :  O-H. . . S-Fe Hydrogen Bond, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Bonisch, C. L. Schmidt, P. Bianco, R. Ladenstein
Ultrahigh-Resolution Study On Pyrococcus Abyssi Rubredoxin: Ii. Introduction Of An O-H. . . Sgamma-Fe Hydrogen Bond Increased The Reduction Potential By 65 Mv.
J. Biol. Inorg. Chem. V. 12 1163 2007
PubMed-ID: 17712580  |  Reference-DOI: 10.1007/S00775-007-0289-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RUB
    Mutation: YES
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Strain: GE5/ORSAY
    Synonym: RD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2NA2Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , CYS A:9 , CYS A:39 , CYS A:42BINDING SITE FOR RESIDUE FE A 54
2AC2SOFTWAREASN A:22 , GLU A:31 , HOH A:205 , HOH A:220 , HOH A:230 , HOH A:254BINDING SITE FOR RESIDUE NA A 200
3AC3SOFTWAREGLU A:31 , HOH A:224 , HOH A:238 , HOH A:250 , HOH A:270 , HOH A:271BINDING SITE FOR RESIDUE NA A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXINPS00202 Rubredoxin signature.RUBR_PYRAB33-43  1A:33-43

(-) Exons   (0, 0)

(no "Exon" information available for 2PYA)

(-) 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:52
 aligned with RUBR_PYRAB | Q9V099 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:52
                                    11        21        31        41        51  
            RUBR_PYRAB    2 AKWRCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAPKSEFERIE 53
               SCOP domains d2pyaa_ A: Rubredoxin                                SCOP domains
               CATH domains 2pyaA00 A:2-53  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains ----Rubredoxin-2pyaA01 A:6-49                   ---- Pfam domains
         Sec.struct. author .eeee.....eee....hhhhh.....hhhhh...........hhh.eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------RUBREDOXIN ---------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  2pya A  2 AKLSCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGSPKSEFERIE 53
                                    11        21        31        41        51
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Rubredoxin (46)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUBR_PYRAB | Q9V099)
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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RUBR_PYRAB | Q9V099: 1yk4 1yk5

(-) Related Entries Specified in the PDB File

1yk4 W4L,R5S
1yk5 WILD TYPE