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(-) Description

Title :  RUBREDOXIN (FORMYL METHIONINE MUTANT) FROM PYROCOCCUS FURIOSUS
 
Authors :  R. Bau, D. C. Rees, D. M. Kurtz, R. A. Scott, H. Huang, M. W. W. Adams, M. K. Eidsness
Date :  22 Aug 98  (Deposition) - 26 Aug 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron-Sulfur Protein, High-Resolution Structure, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Bau, D. C. Rees, D. M. Kurtz, R. A. Scott, H. Huang, M. W. W. Adams, M. K. Eidsness
Crystal Structure Of Rubredoxin From Pyrococcus Furiosus At 0. 95 Angstroms Resolution, And The Structures Of N-Terminal Methionine And Formylmethionine Variants Of Pf Rd. Contributions Of N-Terminal Interactions To Thermostability
J. Biol. Inorg. Chem. V. 3 484 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (RUBREDOXIN)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Other Details: PRODUCT OF A SYNTHETIC PF RD GENE
    Synonym: PF RD
    Variant: FMET

 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
1FE1Ligand/IonFE (III) ION
2FME1Mod. Amino AcidN-FORMYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , CYS A:9 , CYS A:39 , CYS A:42BINDING SITE FOR RESIDUE FE A 55

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BQ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BQ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BQ9)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXIN_LIKEPS50903 Rubredoxin-like domain profile.RUBR_PYRFU1-52  1A:1-52
2RUBREDOXINPS00202 Rubredoxin signature.RUBR_PYRFU33-43  1A:33-43

(-) Exons   (0, 0)

(no "Exon" information available for 1BQ9)

(-) 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:54
 aligned with RUBR_PYRFU | P24297 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:54
                                    10        20        30        40        50    
            RUBR_PYRFU    1 MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 54
               SCOP domains d1bq9a_ A: Rubredoxin                                  SCOP domains
               CATH domains -1bq9A00 A:2-54  [code=2.20.28.10, no name defined]    CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.....eee.....hhh.......hhh.............hhheee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:1-52 UniProt: 1-52          -- PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ----------- PROSITE (2)
                 Transcript ------------------------------------------------------ Transcript
                  1bq9 A  1 mAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 54
                            |       10        20        30        40        50    
                            |                                                     
                            1-FME
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "Pfam Domain" information available for 1BQ9)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUBR_PYRFU | P24297)
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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  RUBR_PYRFU | P24297
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 Related Entries

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

UniProtKB/Swiss-Prot
        RUBR_PYRFU | P24297: 1bq8 1brf 1caa 1cad 1iu5 1iu6 1qcv 1rwd 1vcx 1zrp 2pvx 3kyu 3kyv 3kyw 3kyx 3kyy 3ryg 3rz6 3rzt 3ss2 4ar3 4ar4 4ar5 4ar6 4k9f 5ai2 5ai3 5nw3

(-) Related Entries Specified in the PDB File

1bq8 1caa