Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF FERRITIN (BACTERIOFERRITIN) FROM BRUCELLA MELITENSIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  15 Jan 09  (Deposition) - 03 Feb 09  (Release) - 03 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (12x)
Keywords :  Niaid, Ssgcid, Decode, Ferritin, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Ferritin From Brucella Melitensis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIOFERRITIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BFR, BAB2_0675
    Organism Scientific: BRUCELLA MELITENSIS BIOVAR ABORTUS 2308
    Organism Taxid: 359391
    Strain: BIOVAR ABORTUS 2308

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (12x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric Unit (6, 16)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FE3Ligand/IonFE (III) ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IMD2Ligand/IonIMIDAZOLE
5MG6Ligand/IonMAGNESIUM ION
6NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 36)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
3HEM12Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IMD24Ligand/IonIMIDAZOLE
5MG-1Ligand/IonMAGNESIUM ION
6NA-1Ligand/IonSODIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:19 , ASN A:23 , TRP A:26 , ARG A:45 , MET A:52 , HIS A:53 , FE A:163 , HOH A:258 , ASN B:23 , TRP B:26 , ARG B:45 , MET B:52 , HIS B:53BINDING SITE FOR RESIDUE HEM A 162
02AC2SOFTWAREMET A:52 , HEM A:162 , MET B:52BINDING SITE FOR RESIDUE FE A 163
03AC3SOFTWAREGLU A:18 , GLU A:51 , HIS A:54 , GLU A:127 , IMD A:171BINDING SITE FOR RESIDUE FE A 164
04AC4SOFTWAREHOH A:197 , HOH A:198 , HOH A:199 , HOH A:200 , HOH A:201 , HOH A:202BINDING SITE FOR RESIDUE MG A 165
05AC5SOFTWAREASP A:34 , HOH A:205 , HOH A:206 , HOH A:207 , HOH B:208BINDING SITE FOR RESIDUE MG A 166
06AC6SOFTWAREASP A:109 , HOH A:320 , HOH A:373BINDING SITE FOR RESIDUE MG A 167
07AC7SOFTWAREGLN A:151 , CL A:170 , HOH A:291 , GLN B:151BINDING SITE FOR RESIDUE NA A 168
08AC8SOFTWAREARG A:105 , LYS A:117BINDING SITE FOR RESIDUE CL A 169
09AC9SOFTWAREARG A:148 , NA A:168 , ARG B:148BINDING SITE FOR RESIDUE CL A 170
10BC1SOFTWAREGLU A:18 , ALA A:21 , GLU A:51 , GLU A:94 , ALA A:97 , TYR A:101 , GLU A:127 , FE A:164 , HOH A:278BINDING SITE FOR RESIDUE IMD A 171
11BC2SOFTWAREGLU B:18 , GLU B:51 , HIS B:54 , GLU B:127 , IMD B:167BINDING SITE FOR RESIDUE FE B 162
12BC3SOFTWAREHOH A:192 , HOH A:194 , HOH A:195 , HOH B:191 , HOH B:193 , HOH B:196BINDING SITE FOR RESIDUE MG B 163
13BC4SOFTWAREHOH A:221 , ASP B:34 , HOH B:220 , HOH B:222 , HOH B:223 , HOH B:304BINDING SITE FOR RESIDUE MG B 164
14BC5SOFTWAREHOH A:376 , HOH A:377 , HOH B:216 , HOH B:374 , HOH B:375BINDING SITE FOR RESIDUE MG B 165
15BC6SOFTWAREARG B:105 , LYS B:117BINDING SITE FOR RESIDUE CL B 166
16BC7SOFTWARELEU B:17 , GLU B:18 , ALA B:21 , GLU B:51 , GLU B:94 , ALA B:97 , TYR B:101 , GLU B:127 , FE B:162 , HOH B:303BINDING SITE FOR RESIDUE IMD B 167

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FVB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:-1 -Ser A:0
2Gly B:-1 -Ser B:0

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FVB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FVB)

(-) Exons   (0, 0)

(no "Exon" information available for 3FVB)

(-) 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    
   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:161
 aligned with Q2YKI4_BRUA2 | Q2YKI4 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         Q2YKI4_BRUA2     - --MKGEPKVIERLNEALFLELGAVNQYWLHYRLLNDWGYTRLAKKEREESIEEMHHADKLIDRIIFLEGFPNLQTVSPLRIGQNVKEVLEADLKGEYDARASYKESREICDKLGDYVSKQLFDELLADEEGHIDFLETQLDLLAKIGGERYGQLNAAPADE 159
               SCOP domains d3fvba_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 3fvbA00 A:-1-159  [code=1.20.1260.10, no name defined]                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fvb A  -1 GSMKGEPKVIERLNEALFLELGAVNQYWLHYRLLNDWGYTRLAKKEREESIEEMHHADKLIDRIIFLEGFPNLQTVSPLRIGQNVKEVLEADLKGEYDARASYKESREICDKLGDYVSKQLFDELLADEEGHIDFLETQLDLLAKIGGERYGQLNAAPADE 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q2YKI4_BRUA2 | Q2YKI4 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         Q2YKI4_BRUA2     - --MKGEPKVIERLNEALFLELGAVNQYWLHYRLLNDWGYTRLAKKEREESIEEMHHADKLIDRIIFLEGFPNLQTVSPLRIGQNVKEVLEADLKGEYDARASYKESREICDKLGDYVSKQLFDELLADEEGHIDFLETQLDLLAKIGGERYGQLNAAPADE 159
               SCOP domains d3fvbb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains 3fvbB00 B:-1-159  [code=1.20.1260.10, no name defined]                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fvb B  -1 GSMKGEPKVIERLNEALFLELGAVNQYWLHYRLLNDWGYTRLAKKEREESIEEMHHADKLIDRIIFLEGFPNLQTVSPLRIGQNVKEVLEADLKGEYDARASYKESREICDKLGDYVSKQLFDELLADEEGHIDFLETQLDLLAKIGGERYGQLNAAPADE 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FVB)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2YKI4_BRUA2 | Q2YKI4)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0004322    ferroxidase activity    Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0006826    iron ion transport    The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

 Visualization

(-) Interactive Views

Asymmetric 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:-1 - Ser A:0   [ RasMol ]  
    Gly B:-1 - Ser B:0   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3fvb
    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
  Q2YKI4_BRUA2 | Q2YKI4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q2YKI4_BRUA2 | Q2YKI4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3FVB)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3FVB)