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(-) Description

Title :  CRYSTAL STRUCTURE OF IRON SUPEROXIDE DISMUTASE FROM ANAPLASMA PHAGOCYTOPHILUM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Sep 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Gram-Negative Bacteria, Human Granulocytic Anaplasmosis, Fe, Metalloenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, B. L. Staker, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Iron Superoxide Dismutase From Anaplasma Phagocytophilum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Chains: A, B, C, D
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SODB, APH_0371
    Organism Scientific: ANAPLASMA PHAGOCYTOPHILUM
    Organism Taxid: 212042
    Strain: HZ

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2NA4Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:24 , HIS A:80 , ASP A:165 , HIS A:169 , HOH A:209BINDING SITE FOR RESIDUE FE A 207
2AC2SOFTWAREPRO A:152 , THR A:155 , GLN A:158 , HOH A:235 , HOH A:407BINDING SITE FOR RESIDUE NA A 208
3AC3SOFTWAREHIS B:24 , HIS B:80 , ASP B:165 , HIS B:169 , HOH B:209BINDING SITE FOR RESIDUE FE B 207
4AC4SOFTWAREPRO B:152 , THR B:155 , GLN B:158 , HOH B:222 , HOH B:408BINDING SITE FOR RESIDUE NA B 208
5AC5SOFTWAREHIS C:24 , HIS C:80 , ASP C:165 , HIS C:169 , HOH C:214BINDING SITE FOR RESIDUE FE C 207
6AC6SOFTWAREPRO C:152 , THR C:155 , GLN C:158 , HOH C:268 , HOH C:274BINDING SITE FOR RESIDUE NA C 208
7AC7SOFTWAREHIS D:24 , HIS D:80 , ASP D:165 , HIS D:169 , HOH D:209BINDING SITE FOR RESIDUE FE D 207
8AC8SOFTWAREPRO D:152 , THR D:155 , GLN D:158 , HOH D:217 , HOH D:268 , HOH D:390BINDING SITE FOR RESIDUE NA D 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JS4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:13 -Pro A:14
2Glu B:13 -Pro B:14
3Glu C:13 -Pro C:14
4Glu D:13 -Pro D:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JS4)

(-) Exons   (0, 0)

(no "Exon" information available for 3JS4)

(-) 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:207
 aligned with Q2GKX4_ANAPZ | Q2GKX4 from UniProtKB/TrEMBL  Length:206

    Alignment length:207
                             1                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
         Q2GKX4_ANAPZ     - -MFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
               SCOP domains d3js4a1 A:0-89 automated matches                                                          d3js4a2 A:90-206 automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js4 A   0 SMFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q2GKX4_ANAPZ | Q2GKX4 from UniProtKB/TrEMBL  Length:206

    Alignment length:207
                             1                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
         Q2GKX4_ANAPZ     - -MFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
               SCOP domains d3js4b1 B:0-89 automated matches                                                          d3js4b2 B:90-206 automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js4 B   0 SMFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       


Chain C from PDB  Type:PROTEIN  Length:206
 aligned with Q2GKX4_ANAPZ | Q2GKX4 from UniProtKB/TrEMBL  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
         Q2GKX4_ANAPZ     1 MFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
               SCOP domains d3js4c1 C:1-89 automated matches                                                         d3js4c2 C:90-206 automated matches                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js4 C   1 MFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      


Chain D from PDB  Type:PROTEIN  Length:206
 aligned with Q2GKX4_ANAPZ | Q2GKX4 from UniProtKB/TrEMBL  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
         Q2GKX4_ANAPZ     1 MFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
               SCOP domains d3js4d1 D:1-89 automated matches                                                         d3js4d2 D:90-206 automated matches                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Fe_N-3js4D05 D:1-88                                                                 ----Sod_Fe_C-3js4D01 D:93-200                                                                                   ------ Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-3js4D06 D:1-88                                                                 ----Sod_Fe_C-3js4D02 D:93-200                                                                                   ------ Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-3js4D07 D:1-88                                                                 ----Sod_Fe_C-3js4D03 D:93-200                                                                                   ------ Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-3js4D08 D:1-88                                                                 ----Sod_Fe_C-3js4D04 D:93-200                                                                                   ------ Pfam domains (4)
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js4 D   1 MFELSDLPYEGLEPYISSHLLDRHYNGHHKTYVDVLNKLVVGTEFEGLGNESLGDIVVKAHNSGSAGRAIFNNAAQIWNHDFYWQSMKPNGGGNPPEKLREMIEHSFGSVEGFNNAFTTSGLGQFGSGWVWLVYDEDAKALKVVSTANADSPLLTQGQLPLATMDVWEHAYYLDYLNLRKKYIDVFLEHLLNWDFVLGRLEDAGVL 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JS4)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sod_Fe_C] (46)
(-)
Clan: no clan defined [family: Sod_Fe_N] (46)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q2GKX4_ANAPZ | Q2GKX4)
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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  3js4
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  1.15.1.1
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 Related Entries

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

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