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(-) Description

Title :  NEUTRON CRYSTALLOGRAPHIC STRUCTURE OF THE REDUCED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN TO 1.38 ANGSTROM RESOLUTION.
 
Authors :  M. G. Cuypers, S. A. Mason, M. P. Blakeley, E. P. Mitchell, M. Haertlein, V. T. Forsyth
Date :  20 Apr 12  (Deposition) - 16 Jan 13  (Release) - 22 Mar 17  (Revision)
Method :  NEUTRON DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Electron Transport, Perdeuterated, Monochromatic Neutron Crystallography, Hydronium, Protonation State (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Cuypers, S. A. Mason, M. P. Blakeley, E. P. Mitchell, M. Haertlein V. T. Forsyth
Near-Atomic Resolution Neutron Crystallography On Perdeuterated Pyrococcus Furiosus Rubredoxin: Implication O Hydronium Ions And Protonation State Equilibria In Redox Changes.
Angew. Chem. Int. Ed. Engl. V. 52 1022 2013
PubMed-ID: 23225503  |  Reference-DOI: 10.1002/ANIE.201207071

(-) Compounds

Molecule 1 - RUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Other Details: REDUCED STATE (FE II), HYDRONIUM IONS, CARBOXYLIC DEUTERONS
    Synonym: RD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 111)

Asymmetric Unit (4, 111)
No.NameCountTypeFull Name
1D3O4Ligand/IonTRIDEUTERIOOXIDANIUM
2D8U2Ligand/IonDEUTERIUM(1+)
3DOD104Ligand/Ion
4FE1Ligand/IonFE (III) ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1D3O4Ligand/IonTRIDEUTERIOOXIDANIUM
2D8U2Ligand/IonDEUTERIUM(1+)
3DOD-1Ligand/Ion
4FE-1Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:5 , CYS A:8 , CYS A:38 , CYS A:41BINDING SITE FOR RESIDUE FE A 1054
2AC2SOFTWAREALA A:1 , LYS A:2 , LEU A:51BINDING SITE FOR RESIDUE D3O A 1057
3AC3SOFTWARESER A:24 , PRO A:25BINDING SITE FOR RESIDUE D3O A 1058
4AC4SOFTWAREALA A:16 , DOD A:2036BINDING SITE FOR RESIDUE D3O A 1060

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AR4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AR4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AR4)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXIN_LIKEPS50903 Rubredoxin-like domain profile.RUBR_PYRFU1-52  1A:0-51
2RUBREDOXINPS00202 Rubredoxin signature.RUBR_PYRFU33-43  1A:32-42
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXIN_LIKEPS50903 Rubredoxin-like domain profile.RUBR_PYRFU1-52  1A:0-51
2RUBREDOXINPS00202 Rubredoxin signature.RUBR_PYRFU33-43  1A:32-42

(-) Exons   (0, 0)

(no "Exon" information available for 4AR4)

(-) 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    
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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 d4ar4a_ A: Rubredoxin                                  SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.....eee.....hhhh.....hhhhh...............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:0-51 UniProt: 1-52          -- PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ----------- PROSITE (2)
                 Transcript ------------------------------------------------------ Transcript
                  4ar4 A  0 MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED 53
                                     9        19        29        39        49
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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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AR4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AR4)

(-) Gene Ontology  (4, 4)

Asymmetric 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 1bq9 1brf 1caa 1cad 1iu5 1iu6 1qcv 1rwd 1vcx 1zrp 2pvx 3kyu 3kyv 3kyw 3kyx 3kyy 3ryg 3rz6 3rzt 3ss2 4ar3 4ar5 4ar6 4k9f 5ai2 5ai3 5nw3

(-) Related Entries Specified in the PDB File

1bq8 RUBREDOXIN (METHIONINE MUTANT) FROM PYROCOCCUS FURIOSUS
1bq9 RUBREDOXIN (FORMYL METHIONINE MUTANT) FROM PYROCOCCUS FURIOSUS
1brf RUBREDOXIN (WILD TYPE) FROM PYROCOCCUS FURIOSUS
1caa RUBREDOXIN (OXIDIZED)
1cad RUBREDOXIN (REDUCED)
1iu5 X-RAY CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT FROMPYROCOCCUS FURIOSUS
1iu6 NEUTRON CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT FROMPYROCOCCUS FURIOSUS
1qcv RUBREDOXIN VARIANT (PFRD-XC4) FOLDS WITHOUT IRON
1rwd BACKBONE NMR STRUCTURE OF A MUTANT P. FURIOSUS RUBREDOXINUSING RESIDUAL DIPOLAR COUPLINGS
1vcx NEUTRON CRYSTAL STRUCTURE OF THE WILD TYPE RUBREDOXIN FROMPYROCOCCUS FURIOSUS AT 1.5A RESOLUTION
1zrp RUBREDOXIN (ZN-SUBSTITUTED) (NMR, 40 STRUCTURES)
4ar3 NEAR-ATOMIC RESOLUTION NEUTRON CRYSTALLOGRAPHY ON THE OXIDISED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN.
4ar5 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE OXIDISED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN IN D2O AT 295K (IN QUARTZ CAPILLARY) TO 1.00 ANGSTROM RESOLUTION.
4ar6 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE REDUCED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN AT 295 K ( IN QUARTZ CAPILLARY) TO 0.92 ANGSTROMS RESOLUTION.