Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  RUBREDOXIN FROM DESULFOVIBRIO VULGARIS REFINED ANISOTROPICALLY AT 0.92 ANGSTROMS RESOLUTION
 
Authors :  Z. Dauter, S. Butterworth, L. C. Sieker, G. Sheldrick, K. S. Wilson
Date :  21 Dec 97  (Deposition) - 16 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron-Sulfur Protein, Rubredoxin, Atomic Resolution, Anisotropic Refinement (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Dauter, S. Butterworth, L. C. Sieker, G. Sheldrick, K. S. Wilson
Anisotropic Refinement Of Rubredoxin From Desulfovibrio Vulgaris
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2FME1Mod. Amino AcidN-FORMYLMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , CYS A:9 , CYS A:39 , CYS A:42BINDING SITE FOR RESIDUE FE2 A 54
2AC2SOFTWARELYS A:3 , ALA A:35 , TRP A:37 , PRO A:45 , LYS A:46 , SER A:47 , HOH A:85 , HOH A:95 , HOH A:96 , HOH A:103 , HOH A:125 , HOH A:126 , HOH A:146BINDING SITE FOR RESIDUE SO4 A 56

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RB9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RB9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RB9)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXIN_LIKEPS50903 Rubredoxin-like domain profile.RUBR_DESVH1-52  1A:1-52
2RUBREDOXINPS00202 Rubredoxin signature.RUBR_DESVH33-43  1A:33-43

(-) Exons   (0, 0)

(no "Exon" information available for 1RB9)

(-) 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_DESVH | P00269 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:52
                                    10        20        30        40        50  
            RUBR_DESVH    1 MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA 52
               SCOP domains d1rb9a_ A: Rubredoxin                                SCOP domains
               CATH domains -1rb9A00 A:2-52  [code=2.20.28.10, no name defined]  CATH domains
               Pfam domains --Rubredoxin-1rb9A01 A:3-49                      --- Pfam domains
     Sec.struct. author (1) ...eee.............hhh.......hhh...........---hh---. Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------eeeeeeee- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:1-52 UniProt: 1-52           PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN --------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                  1rb9 A  1 mKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA 52
                            |       10        20        30        40        50  
                            |                                                   
                            1-FME
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUBR_DESVH | P00269)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rb9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1rb9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RUBR_DESVH | P00269
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RUBR_DESVH | P00269
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RUBR_DESVH | P00269: 2kkd 2ql0 7rxn 8rxn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RB9)