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(-) Description

Title :  CRYSTAL STRUCTURE OF A NITROREDUCTASE FAMILY PROTEIN FROM AGROBACTERIUM TUMEFACIENS STR. C58
 
Authors :  K. Tan, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  08 Oct 09  (Deposition) - 27 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apc5990, Nitroreductase Family, Agrobacterium Tumefaciens Str. C58, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of A Nitroreductase Family Protein From Agrobacterium Tumefaciens Str. C58
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITROREDUCTASE FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AGR_C_3200, ATU1744
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO47Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:17 , FMN B:200BINDING SITE FOR RESIDUE SO4 B 196
2AC2SOFTWARESER A:30 , LYS A:31 , ARG A:59BINDING SITE FOR RESIDUE SO4 A 196
3AC3SOFTWAREARG B:92BINDING SITE FOR RESIDUE SO4 B 197
4AC4SOFTWAREARG A:17 , PRO A:20 , FMN A:199 , SO4 B:199BINDING SITE FOR RESIDUE SO4 A 197
5AC5SOFTWAREARG A:92 , GLU A:144BINDING SITE FOR RESIDUE SO4 A 198
6AC6SOFTWARESER B:30 , LYS B:31 , ARG B:59BINDING SITE FOR RESIDUE SO4 B 198
7AC7SOFTWARESO4 A:197 , FMN A:199 , HIS B:47 , GLY B:48 , LYS B:49BINDING SITE FOR RESIDUE SO4 B 199
8AC8SOFTWAREVAL A:44 , PRO A:45 , ASP A:46 , HIS A:47 , MSE A:119 , ARG B:16 , ARG B:17 , SER B:18 , ASN B:140 , TRP B:141 , THR B:143 , GLU B:144 , ARG B:180 , ARG B:182 , SO4 B:196BINDING SITE FOR RESIDUE FMN B 200
9AC9SOFTWAREARG A:16 , ARG A:17 , SER A:18 , ASN A:140 , TRP A:141 , LEU A:142 , THR A:143 , GLU A:144 , ARG A:180 , ARG A:182 , SO4 A:197 , VAL B:44 , PRO B:45 , ASP B:46 , HIS B:47 , MSE B:119 , SO4 B:199BINDING SITE FOR RESIDUE FMN A 199

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:26 -Pro A:27
2Glu B:26 -Pro B:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K6H)

(-) Exons   (0, 0)

(no "Exon" information available for 3K6H)

(-) 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:191
 aligned with A9CIP6_AGRFC | A9CIP6 from UniProtKB/TrEMBL  Length:193

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
         A9CIP6_AGRFC     2 TSDIKLLDYLRVRRSTPALQLSEPGPSKGEIEEILRLAVRVPDHGKLAPWRFVVYRGEERVRLSEAALRIALEKNPDLDLQQQEAERTRFTRAPVVIAVISTAKPHFKIPEWEQVMSAGAVCLNVIFAANASGFAANWLTEWLAFDPAFLAEIGVSAEEKVAGYIHIGSTTFPPVERPRPELADVVTWVGD 192
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...............hhhhhhhhhhhhh..........eeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh.....eeeeeeeee............hhhhheeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6h A   4 TSDIKLLDYLRVRRSTPALQLSEPGPSKGEIEEILRLAVRVPDHGKLAPWRFVVYRGEERVRLSEAALRIALEKNPDLDLQQQEAERTRFTRAPVVIAVISTAKPHFKIPEWEQVmSAGAVCLNVIFAANASGFAANWLTEWLAFDPAFLAEIGVSAEEKVAGYIHIGSTTFPPVERPRPELADVVTWVGD 194
                                    13        23        33        43        53        63        73        83        93       103       113     | 123       133       143       153       163       173       183       193 
                                                                                                                                             119-MSE                                                                       


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with A9CIP6_AGRFC | A9CIP6 from UniProtKB/TrEMBL  Length:193

    Alignment length:191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
         A9CIP6_AGRFC     3 SDIKLLDYLRVRRSTPALQLSEPGPSKGEIEEILRLAVRVPDHGKLAPWRFVVYRGEERVRLSEAALRIALEKNPDLDLQQQEAERTRFTRAPVVIAVISTAKPHFKIPEWEQVMSAGAVCLNVIFAANASGFAANWLTEWLAFDPAFLAEIGVSAEEKVAGYIHIGSTTFPPVERPRPELADVVTWVGDV 193
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...hhhhh.....hhhhhhhhhhhhh...hhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......eeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh.....eeeeeeeee............hhhhheeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6h B   5 SDIKLLDYLRVRRSTPALQLSEPGPSKGEIEEILRLAVRVPDHGKLAPWRFVVYRGEERVRLSEAALRIALEKNPDLDLQQQEAERTRFTRAPVVIAVISTAKPHFKIPEWEQVmSAGAVCLNVIFAANASGFAANWLTEWLAFDPAFLAEIGVSAEEKVAGYIHIGSTTFPPVERPRPELADVVTWVGDV 195
                                    14        24        34        44        54        64        74        84        94       104       114    |  124       134       144       154       164       174       184       194 
                                                                                                                                            119-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3K6H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K6H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3K6H)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A9CIP6_AGRFC | A9CIP6)
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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