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 :  CRYSTAL STRUCTURE OF F25H FERREDOXIN 1 MUTANT FROM AZOTOBACTER VINELANDII AT 1.75 ANGSTROM RESOLUTION
 
Authors :  K. Chen, C. A. Bonagura, G. J. Tilley, Y. S. Jung, F. A. Armstrong, C. D. Stout, B. K. Burgess
Date :  13 Jun 00  (Deposition) - 28 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Sheet, Protein Monomer, Iron Sulfur Protein, Ferredoxin, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Chen, C. A. Bonagura, G. J. Tilley, J. P. Mcevoy, Y. S. Jung, F. A. Armstrong, C. D. Stout, B. K. Burgess
Crystal Structures Of Ferredoxin Variants Exhibiting Large Changes In [Fe-S] Reduction Potential.
Nat. Struct. Biol. V. 9 188 2002
PubMed-ID: 11875515
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERREDOXIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKT230
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 354
    Synonym: FDI

 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
1F3S1Ligand/IonFE3-S4 CLUSTER
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:79 , ASN A:80 , HOH A:389 , HOH A:413BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWAREVAL A:4 , CYS A:8 , LYS A:12 , TYR A:13 , THR A:14 , ASP A:15 , CYS A:16 , LEU A:32 , CYS A:49BINDING SITE FOR RESIDUE F3S A 200
3AC3SOFTWAREPHE A:2 , CYS A:20 , VAL A:22 , CYS A:24 , HIS A:25 , ILE A:34 , CYS A:39 , ILE A:40 , CYS A:42 , ALA A:43 , CYS A:45BINDING SITE FOR RESIDUE SF4 A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F5C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F5C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F5C)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER1_AZOVI31-60
1-30		  1A:30-59
-
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.FER1_AZOVI40-51  1A:39-50

(-) Exons   (0, 0)

(no "Exon" information available for 1F5C)

(-) 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:106
 aligned with FER1_AZOVI | P00214 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           FER1_AZOVI     2 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 107
               SCOP domains d1f5ca_ A: Ferredoxin                                                                                      SCOP domains
               CATH domains 1f5cA00 A:1-106  [code=3.30.70.20, no name defined]                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhh...............eeee..eeee..........hhhhh....eee.hhhhhhhhhhhhhhhhhh..............hhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -          4FE4S_FER_2  PDB: A:30-59     ----------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------4FE4S_FER_1 -------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1f5c A   1 AFVVTDNCIKCKYTDCVEVCPVDCHYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER 106
                                    10        20        30        40        50        60        70        80        90       100
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F5C)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FER1_AZOVI | P00214)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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.

 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
    F3S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f5c)
 

(-) 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
  1f5c
    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
  FER1_AZOVI | P00214
    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
  FER1_AZOVI | P00214
    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
        FER1_AZOVI | P00214: 1a6l 1axq 1b0t 1b0v 1d3w 1f5b 1fd2 1fda 1fdb 1fdd 1fer 1ff2 1frh 1fri 1frj 1frk 1frl 1frm 1frx 1ftc 1g3o 1g6b 1gao 1pc4 1pc5 2fd2 5fd1 6fd1 6fdr 7fd1 7fdr

(-) Related Entries Specified in the PDB File

1d3w X-RAY CRYSTAL STRUCTURE OF FERREDOXIN 1 D15E MUTANT FROM AZOTOBACTER VINELANDII AT 1.7 ANGSTROM RESOLUTION
1f5c X-RAY CRYSTAL STRUCTURE OF FERREDOXIN 1 F25H MUTANT FROM AZOTOBACTER VINELANDII AT 1.75 ANGSTROM RESOLUTION
1fdd X-RAY CRYSTAL STRUCTURE OF FERREDOXIN 1 D15N MUTANT FROM AZOTOBACTER VINELANDII AT 1.9 ANGSTROM RESOLUTION
6fdr X-RAY CRYSTAL STRUCTURE OF DITHIONITE REDUCED FERREDOXIN 1 WILDTYPE FROM AZOTOBACTER VINELANDII AT 1.4 ANGSTROM RESOLUTION
7fdr X-RAY CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF FERREDOXIN 1 WILDTYPE FROM AZOTOBACTER VINELANDII AT 1.4 ANGSTROM RESOLUTION