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(-) Description

Title :  X-RAY STRUCTURE OF OXIDOREDUCTASE FROM CORYNEBACTERIUM DIPHTHERIAE,HEXAGONAL CRYSTAL FORM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET CDR100D
 
Authors :  A. Kuzin, S. Lew, S. Sahdev, R. Xiao, C. Ciccosanti, H. Wang, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  29 Sep 09  (Deposition) - 20 Oct 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Crystal Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Cdr100D, Q6Ngsi_cordi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, S. Lew, J. Seetharaman, S. Sahdev, R. Xiao, C. Ciccosanti, H. Wang, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Cdr100D
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXIDOREDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 14-15C
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DIP1437
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 40)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2SO416Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , LEU A:11 , SER A:12 , SER A:15 , SER A:16 , THR A:17 , PRO A:84BINDING SITE FOR RESIDUE SO4 A 182
2AC2SOFTWAREGLY A:118 , SER A:119 , ARG A:121BINDING SITE FOR RESIDUE SO4 A 183
3AC3SOFTWARELYS A:87 , THR A:103 , TYR A:136 , HOH A:213BINDING SITE FOR RESIDUE SO4 A 184
4AC4SOFTWAREARG A:138 , ARG A:167BINDING SITE FOR RESIDUE SO4 A 185

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K20)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K20)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K20)

(-) Exons   (0, 0)

(no "Exon" information available for 3K20)

(-) 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:181
 aligned with Q6NGS1_CORDI | Q6NGS1 from UniProtKB/TrEMBL  Length:221

    Alignment length:181
                             1                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 
         Q6NGS1_CORDI     - -MRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLMTAMTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKMFFDILDTDALTGMPTIIAATAGSARHSLVLDYALRPLLSYMRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -FMN_red-3k20A01 A:1-154                                                                                                                                   -------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh....hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhh.........eeeeeeee......hhhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k20 A   0 HmRTLAVISAGLSTPSSTRQIADSISEAVTAAVSARGEALSVSTIELSELIPDLmTAmTTRVHTTKLEEITSALSASDGLVVATPVFKASYTGLFKmFFDILDTDALTGmPTIIAATAGSARHSLVLDYALRPLLSYmRAVVVPTGVFAATEDFGGPEGAEFNKRIARAAGELASLIVEES 180
                             |       9        19        29        39        49    |  |59        69        79        89      | 99       109       119       129       139       149       159       169       179 
                             |                                                   54-MSE                                    96-MSE      109-MSE                     137-MSE                                       
                             1-MSE                                                  57-MSE
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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 3K20)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K20)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q6NGS1_CORDI | Q6NGS1)
molecular function
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q6NGS1_CORDI | Q6NGS1: 3k1y

(-) Related Entries Specified in the PDB File

2vzj 36% OF AMINO ACID RESIDUES ARE IDENTICAL. RELATED ID: CDR100D RELATED DB: TARGETDB