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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIOFERRITIN FROM R.SPHAEROIDES
 
Authors :  K. Y. Hwang, K. H. Nam
Date :  31 Mar 09  (Deposition) - 22 Dec 09  (Release) - 05 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (8x)
Keywords :  Bacterioferritin, Ferritin, Iron Storage, Di-Iron, Ferroxidase Activity, Heme, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Nam, Y. Xu, S. Piao, A. Priyadarshi, E. H. Lee, H. -Y. Kim, Y. H. Jeon, N. -C. Ha, K. Y. Hwang
Crystal Structure Of Bacterioferritin From Rhodobacter Sphaeroides
Biochem. Biophys. Res. Commun. V. 391 990 2010
PubMed-ID: 19968959  |  Reference-DOI: 10.1016/J.BBRC.2009.12.003

(-) Compounds

Molecule 1 - BACTERIOFERRITIN
    Chains: A, B, C
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 272943
    Other Details: NATIVE PROTEIN AS-ISOLATED
    Strain: 2.4.1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (8x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FE3Ligand/IonFE (III) ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2HEM16Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:19 , TRP A:26 , ARG A:45 , MET A:52 , HIS A:53 , TRP C:26 , MET C:52 , HIS C:53 , ALA C:55BINDING SITE FOR RESIDUE HEM A 162
2AC2SOFTWARELEU B:19 , TRP B:26 , ARG B:45 , MET B:52 , HIS B:53 , ALA B:55BINDING SITE FOR RESIDUE HEM B 162
3AC3SOFTWAREGLU B:18 , GLU B:51 , HIS B:54 , GLU B:127BINDING SITE FOR RESIDUE FE B 163
4AC4SOFTWAREGLU A:18 , GLU A:51 , HIS A:54 , GLU A:127BINDING SITE FOR RESIDUE FE A 163
5AC5SOFTWAREGLU C:18 , GLU C:51 , HIS C:54 , GLU C:127BINDING SITE FOR RESIDUE FE C 162

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GVY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GVY)

(-) 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:157
 aligned with Q3J696_RHOS4 | Q3J696 from UniProtKB/TrEMBL  Length:161

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q3J696_RHOS4     1 MQGDAKVIEYLNAALRSELTAVSQYWLHYRLQEDWGFGSIAHKSRKESIEEMHHADKLIQRIIFLGGHPNLQRLNPLRIGQTLRETLDADLAAEHDARTLYIEARDHCEKVRDYPSKMLFEELIADEEGHIDYLETQIDLMGSIGEQNYGMLNAKPA 157
               SCOP domains d3gvya_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains 3gvyA00 A:1-157  [code=1.20.1260.10, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvy A   1 MQGDAKVIEYLNAALRSELTAVSQYWLHYRLQEDWGFGSIAHKSRKESIEEMHHADKLIQRIIFLGGHPNLQRLNPLRIGQTLRETLDADLAAEHDARTLYIEARDHCEKVRDYPSKMLFEELIADEEGHIDYLETQIDLMGSIGEQNYGMLNAKPA 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with Q3J696_RHOS4 | Q3J696 from UniProtKB/TrEMBL  Length:161

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q3J696_RHOS4     1 MQGDAKVIEYLNAALRSELTAVSQYWLHYRLQEDWGFGSIAHKSRKESIEEMHHADKLIQRIIFLGGHPNLQRLNPLRIGQTLRETLDADLAAEHDARTLYIEARDHCEKVRDYPSKMLFEELIADEEGHIDYLETQIDLMGSIGEQNYGMLNAKPAD 158
               SCOP domains d3gvyb_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains 3gvyB00 B:1-158  [code=1.20.1260.10, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvy B   1 MQGDAKVIEYLNAALRSELTAVSQYWLHYRLQEDWGFGSIAHKSRKESIEEMHHADKLIQRIIFLGGHPNLQRLNPLRIGQTLRETLDADLAAEHDARTLYIEARDHCEKVRDYPSKMLFEELIADEEGHIDYLETQIDLMGSIGEQNYGMLNAKPAD 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        


Chain C from PDB  Type:PROTEIN  Length:158
 aligned with Q3J696_RHOS4 | Q3J696 from UniProtKB/TrEMBL  Length:161

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q3J696_RHOS4     1 MQGDAKVIEYLNAALRSELTAVSQYWLHYRLQEDWGFGSIAHKSRKESIEEMHHADKLIQRIIFLGGHPNLQRLNPLRIGQTLRETLDADLAAEHDARTLYIEARDHCEKVRDYPSKMLFEELIADEEGHIDYLETQIDLMGSIGEQNYGMLNAKPAD 158
               SCOP domains d3gvyc_ C: automated matches                                                                                                                                   SCOP domains
               CATH domains 3gvyC00 C:1-158  [code=1.20.1260.10, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvy C   1 MQGDAKVIEYLNAALRSELTAVSQYWLHYRLQEDWGFGSIAHKSRKESIEEMHHADKLIQRIIFLGGHPNLQRLNPLRIGQTLRETLDADLAAEHDARTLYIEARDHCEKVRDYPSKMLFEELIADEEGHIDYLETQIDLMGSIGEQNYGMLNAKPAD 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q3J696_RHOS4 | Q3J696)
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.

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