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(-) Description

Title :  STRUCTURE OF THE SUPEROXIDE DISMUTASE (FE) (SODB) FROM COXIELLA BURNETII
 
Authors :  M. C. Franklin, J. Cheung, M. Cassidy, J. Love
Date :  09 Sep 11  (Deposition) - 21 Sep 11  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Superoxide Dismutase (Fe), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [FE]
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CBU_1708, SODB
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 777
    Strain: RSA 493 NINE MILE PHASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FE22Ligand/IonFE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , HIS A:74 , ASP A:157 , HIS A:161 , HOH A:404BINDING SITE FOR RESIDUE FE2 A 1001
2AC2SOFTWAREHIS B:27 , HIS B:74 , ASP B:157 , HIS B:161 , HOH B:355BINDING SITE FOR RESIDUE FE2 B 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:16 -Pro A:17
2Glu B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_COXBU157-164
 		  2A:157-164
B:157-164

(-) Exons   (0, 0)

(no "Exon" information available for 3TQJ)

(-) 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:192
 aligned with SODF_COXBU | P19685 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_COXBU     2 AFELPDLPYKLNALEPHISQETLEYHHGKHHRAYVNKLNKLIEGTPFEKEPLEEIIRKSDGGIFNNAAQHWNHTFYWHCMSPDGGGDPSGELASAIDKTFGSLEKFKALFTDSANNHFGSGWAWLVKDNNGKLEVLSTVNARNPMTEGKKPLMTCDVWEHAYYIDTRNDRPKYVNNFWQVVNWDFVMKNFKS 193
               SCOP domains d3tqja1 A:2-83 automated matches                                                  d3tqja2 A:84-193 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tqj A   2 AFELPDLPYKLNALEPHISQETLEYHHGKHHRAYVNKLNKLIEGTPFEKEPLEEIIRKSDGGIFNNAAQHWNHTFYWHCMSPDGGGDPSGELASAIDKTFGSLEKFKALFTDSANNHFGSGWAWLVKDNNGKLEVLSTVNARNPMTEGKKPLMTCDVWEHAYYIDTRNDRPKYVNNFWQVVNWDFVMKNFKS 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with SODF_COXBU | P19685 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_COXBU     2 AFELPDLPYKLNALEPHISQETLEYHHGKHHRAYVNKLNKLIEGTPFEKEPLEEIIRKSDGGIFNNAAQHWNHTFYWHCMSPDGGGDPSGELASAIDKTFGSLEKFKALFTDSANNHFGSGWAWLVKDNNGKLEVLSTVNARNPMTEGKKPLMTCDVWEHAYYIDTRNDRPKYVNNFWQVVNWDFVMKNFKS 193
               SCOP domains d3tqjb1 B:2-83 automated matches                                                  d3tqjb2 B:84-193 automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhh.eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tqj B   2 AFELPDLPYKLNALEPHISQETLEYHHGKHHRAYVNKLNKLIEGTPFEKEPLEEIIRKSDGGIFNNAAQHWNHTFYWHCMSPDGGGDPSGELASAIDKTFGSLEKFKALFTDSANNHFGSGWAWLVKDNNGKLEVLSTVNARNPMTEGKKPLMTCDVWEHAYYIDTRNDRPKYVNNFWQVVNWDFVMKNFKS 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TQJ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SODF_COXBU | P19685)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
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.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

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  3tqj
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 Related Entries

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