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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE OXYGENASE (SO_2589) FROM SHEWANELLA ONEIDENSIS AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  27 Aug 10  (Deposition) - 15 Sep 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Oxygenase (So_2589) From Shewanella Oneidensis At 2. 20 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, IRON/ASCORBATE FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SO_2589
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 38)

Asymmetric/Biological Unit (4, 38)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3MSE27Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:272 , ARG D:272BINDING SITE FOR RESIDUE CL A 281
02AC2SOFTWARESER A:256 , GOL A:287 , ASN B:61BINDING SITE FOR RESIDUE CL A 283
03AC3SOFTWAREASN A:145 , HIS A:254 , CL A:283 , HOH A:703 , GLY B:95 , ARG B:102 , HOH B:301 , HOH B:476BINDING SITE FOR RESIDUE GOL A 287
04AC4SOFTWAREARG B:272 , HOH B:903 , ARG C:272BINDING SITE FOR RESIDUE CL B 280
05AC5SOFTWAREASP B:7 , ARG B:16 , HOH C:455BINDING SITE FOR RESIDUE CL B 282
06AC6SOFTWAREASN A:61 , SER B:256BINDING SITE FOR RESIDUE CL B 284
07AC7SOFTWAREGLU B:187 , ARG B:244 , SER B:246 , HOH B:568 , HOH B:578 , HOH B:760 , HOH B:924BINDING SITE FOR RESIDUE GOL B 288
08AC8SOFTWARESER C:256 , ASN D:61BINDING SITE FOR RESIDUE CL C 286
09AC9SOFTWARETYR C:109 , GLU C:110 , ASN C:113 , THR C:114 , SER C:117BINDING SITE FOR RESIDUE PEG C 290
10BC1SOFTWAREASN C:61 , SER D:256BINDING SITE FOR RESIDUE CL D 285
11BC2SOFTWAREHIS A:65 , PHE A:69 , ARG C:62 , MSE D:270 , ARG D:274BINDING SITE FOR RESIDUE GOL D 289

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ON7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ON7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ON7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ON7)

(-) Exons   (0, 0)

(no "Exon" information available for 3ON7)

(-) 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:269
 aligned with Q8EE01_SHEON | Q8EE01 from UniProtKB/TrEMBL  Length:279

    Alignment length:277
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       
         Q8EE01_SHEON     3 LETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFMFNRETHDGFFPASISETAKGHTVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEMIANSHKTLLRILHYPPMTGDEEMGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDMLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLMERLRELGVL 279
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.......eee...--------......eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhh.....eeeeeee...........eeeeee.....eeeee......eeee.....eee.......eeeeehhhhhhhh........eeee..........eee..eee............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on7 A   3 LETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFmFNRETHDGFFPAS--------TVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEmIANSHKTLLRILHYPPmTGDEEmGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDmLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLmERLRELGVL 279
                                    12        22        32        42        52      | 62        72        82        92       102       112       122       132       142       152      |162  |    172       182       192       202       212   |   222       232       242       252       262       272       
                                                                                   59-MSE       72       81                                                          142-MSE          159-MSE |                                                216-MSE                                               270-MSE     
                                                                                                                                                                                            165-MSE                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with Q8EE01_SHEON | Q8EE01 from UniProtKB/TrEMBL  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         Q8EE01_SHEON     1 MKLETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFMFNRETHDGFFPASISETAKGHTVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEMIANSHKTLLRILHYPPMTGDEEMGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDMLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLMERLRELGVL 279
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....hhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.......eee....ee.....ee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhh.....eeeeeee...........eeeeee.....eeeee......eeee.....eee.......eeeeehhhhhhhh........eeee..........eee..eee............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on7 B   1 mKLETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFmFNRETHDGFFPASISETAKGHTVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEmIANSHKTLLRILHYPPmTGDEEmGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDmLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLmERLRELGVL 279
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140 |     150       160    |  170       180       190       200       210     | 220       230       240       250       260       270         
                            1-MSE                                                    59-MSE                                                                            142-MSE          159-MSE |                                                216-MSE                                               270-MSE     
                                                                                                                                                                                              165-MSE                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:270
 aligned with Q8EE01_SHEON | Q8EE01 from UniProtKB/TrEMBL  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         Q8EE01_SHEON     1 MKLETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFMFNRETHDGFFPASISETAKGHTVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEMIANSHKTLLRILHYPPMTGDEEMGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDMLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLMERLRELGVL 279
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....hhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhh.hhhhhhh.......eee...---------.....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhh.....eeeeeee...........eeeeee.....eeeee......eeee.....eee.......eeeeehhhhhhhh........eeee..........eee..eee............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on7 C   1 mKLETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFmFNRETHDGFFPAS---------VKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEmIANSHKTLLRILHYPPmTGDEEmGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDmLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLmERLRELGVL 279
                            |       10        20        30        40        50        60        70 |       - |      90       100       110       120       130       140 |     150       160    |  170       180       190       200       210     | 220       230       240       250       260       270         
                            1-MSE                                                    59-MSE       72        82                                                         142-MSE          159-MSE |                                                216-MSE                                               270-MSE     
                                                                                                                                                                                              165-MSE                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:273
 aligned with Q8EE01_SHEON | Q8EE01 from UniProtKB/TrEMBL  Length:279

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         Q8EE01_SHEON     1 MKLETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFMFNRETHDGFFPASISETAKGHTVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEMIANSHKTLLRILHYPPMTGDEEMGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDMLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLMERLRELGVL 279
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DIOX_N-3on7D05 D:3-117                                                                                             -----------------------------2OG-FeII_Oxy-3on7D01 D:147-253                                                                             -------------------------- Pfam domains (1)
           Pfam domains (2) --DIOX_N-3on7D06 D:3-117                                                                                             -----------------------------2OG-FeII_Oxy-3on7D02 D:147-253                                                                             -------------------------- Pfam domains (2)
           Pfam domains (3) --DIOX_N-3on7D07 D:3-117                                                                                             -----------------------------2OG-FeII_Oxy-3on7D03 D:147-253                                                                             -------------------------- Pfam domains (3)
           Pfam domains (4) --DIOX_N-3on7D08 D:3-117                                                                                             -----------------------------2OG-FeII_Oxy-3on7D04 D:147-253                                                                             -------------------------- Pfam domains (4)
         Sec.struct. author ....eee....hhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.......eee....------.......eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhh.....eeeeeee...........eeeeee.....eeeee......eeee.....eee.......eeeeehhhhhhhh........eeee..........eee..eee............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on7 D   1 mKLETIDYRAADSAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNSEAKNEFmFNRETHDGFFPASI------HTVKDIKEYYHVYPWGRIPDSLRANILAYYEKANTLASELLEWIETYSPDEIKAKFSIPLPEmIANSHKTLLRILHYPPmTGDEEmGAIRAAAHEDINLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDmLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSERYTADSYLmERLRELGVL 279
                            |       10        20        30        40        50        60        70  |     80        90       100       110       120       130       140 |     150       160    |  170       180       190       200       210     | 220       230       240       250       260       270         
                            1-MSE                                                    59-MSE        73     80                                                           142-MSE          159-MSE |                                                216-MSE                                               270-MSE     
                                                                                                                                                                                              165-MSE
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 3ON7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ON7)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)
(-)
Clan: no clan defined [family: DIOX_N] (24)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8EE01_SHEON | Q8EE01)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    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.
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.

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