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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE OXIDOREDUCTASE (YP_213212.1) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.99 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  26 Sep 08  (Deposition) - 14 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Yp_213212. 1, Putative Oxidoreductase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Oxidoreductase (Yp_213212. 1) From Bacteroides Fragilis Nctc 9343 At 1. 99 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_213212.1, BF3618
    Organism Scientific: BACTEROIDES FRAGILIS NCTC 9343
    Organism Taxid: 272559

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , ARG A:9 , THR A:10 , ARG A:12 , GLN A:64 , MSE A:66 , CYS A:128 , TYR A:129 , LEU A:130 , GLY A:131 , VAL A:168 , ARG A:170 , HOH A:547 , HOH A:548 , HOH A:549 , HOH A:595 , SER B:35 , THR B:36 , MSE B:37 , GLY B:39 , LEU B:111BINDING SITE FOR RESIDUE FMN A 300
2AC2SOFTWARESER A:35 , THR A:36 , MSE A:37 , LEU A:111 , ARG B:8 , ARG B:9 , THR B:10 , ARG B:12 , GLN B:64 , MSE B:66 , CYS B:128 , TYR B:129 , LEU B:130 , GLY B:131 , VAL B:168 , ARG B:170 , HOH B:324 , HOH B:339 , HOH B:390 , HOH B:402 , HOH B:428BINDING SITE FOR RESIDUE FMN B 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EOF)

(-) 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:248
 aligned with Q5L9C9_BACFN | Q5L9C9 from UniProtKB/TrEMBL  Length:247

    Alignment length:248
                             1                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
         Q5L9C9_BACFN     - -MMDTVKNRRTIRKYQQKDITPDLLNDLLETSFRASTMGGMQLYSVVVTRDAEKKEILSPAHFNQPMVKEAPVVLTFCADFRRFCKYCQERNAVPGYGNLMSFLNAAMDTLLVAQTFCTLAEEAGLGICYLGTTTYNPQMIIDALHLPELVFPITTVTVGYPAESPKQVDRLPIEGIIHEESYHDYTAEDINRLYAYKESLPENKLFIEENQKETLPQVFTDVRYTKKDNEFMSENLLKVLRRQGFMD 247
               SCOP domains d3eofa_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhh......hhhhhh.eeeeeeeehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh....eeeeeeeeee............hhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eof A   0 GmmDTVKNRRTIRKYQQKDITPDLLNDLLETSFRASTmGGmQLYSVVVTRDAEKKEILSPAHFNQPmVKEAPVVLTFCADFRRFCKYCQERNAVPGYGNLmSFLNAAmDTLLVAQTFCTLAEEAGLGICYLGTTTYNPQmIIDALHLPELVFPITTVTVGYPAESPKQVDRLPIEGIIHEESYHDYTAEDINRLYAYKESLPENKLFIEENQKETLPQVFTDVRYTKKDNEFmSENLLKVLRRQGFmD 247
                             ||      9        19        29       |39|       49        59      | 69        79        89        99|      109       119       129       139       149       159       169       179       189       199       209       219       229  |    239      | 
                             ||                                 37-MSE                       66-MSE                           100-MSE  |                             139-MSE                                                                                      232-MSE       246-MSE
                             1-MSE                                 40-MSE                                                            107-MSE                                                                                                                                        
                              2-MSE                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with Q5L9C9_BACFN | Q5L9C9 from UniProtKB/TrEMBL  Length:247

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
         Q5L9C9_BACFN     2 MDTVKNRRTIRKYQQKDITPDLLNDLLETSFRASTMGGMQLYSVVVTRDAEKKEILSPAHFNQPMVKEAPVVLTFCADFRRFCKYCQERNAVPGYGNLMSFLNAAMDTLLVAQTFCTLAEEAGLGICYLGTTTYNPQMIIDALHLPELVFPITTVTVGYPAESPKQVDRLPIEGIIHEESYHDYTAEDINRLYAYKESLPENKLFIEENQKETLPQVFTDVRYTKKDNEFMSENLLKVLRRQGFMD 247
               SCOP domains d3eofb_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh............hhhhhhhhhhhhh...hhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhh.eeeeeeeehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh....eeeeeeeeee............hhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eof B   2 mDTVKNRRTIRKYQQKDITPDLLNDLLETSFRASTmGGmQLYSVVVTRDAEKKEILSPAHFNQPmVKEAPVVLTFCADFRRFCKYCQERNAVPGYGNLmSFLNAAmDTLLVAQTFCTLAEEAGLGICYLGTTTYNPQmIIDALHLPELVFPITTVTVGYPAESPKQVDRLPIEGIIHEESYHDYTAEDINRLYAYKESLPENKLFIEENQKETLPQVFTDVRYTKKDNEFmSENLLKVLRRQGFmD 247
                            |       11        21        31     |  41        51        61    |   71        81        91       101     | 111       121       131       141       151       161       171       181       191       201       211       221       231|      241    | 
                            |                                 37-MSE                       66-MSE                           100-MSE  |                             139-MSE                                                                                      232-MSE       246-MSE
                            2-MSE                                40-MSE                                                            107-MSE
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5L9C9_BACFN | Q5L9C9)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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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