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(-) Description

Title :  NEUTRON CRYSTAL STRUCTURE OF DISSIMILATORY SULFITE REDUCTASE D (DSRD)
 
Authors :  T. Chatake, N. Mizuno, G. Voordouw, Y. Higuchi, S. Arai, I. Tanaka, N. Ni
Date :  19 Sep 04  (Deposition) - 19 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  NEUTRON DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Neutron Hydrogen Hydration Protein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Chatake, N. Mizuno, G. Voordouw, Y. Higuchi, S. Arai, I. Tanaka, N. Niimura
Crystallization And Preliminary Neutron Analysis Of The Dissimilatory Sulfite Reductase D (Dsrd) Protein From The Sulfate-Reducing Bacterium Desulfovibrio Vulgaris.
Acta Crystallogr. , Sect. D V. 59 2306 2003
PubMed-ID: 14646103  |  Reference-DOI: 10.1107/S0907444903020596
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DSVD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 881
    Synonym: DISSIMILATORY SULFITE REDUCTASE D

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 100)

Asymmetric/Biological Unit (2, 100)
No.NameCountTypeFull Name
1DOD99Ligand/Ion
2SO41Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 1WQ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WQ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WQ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WQ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WQ2)

(-) Exons   (0, 0)

(no "Exon" information available for 1WQ2)

(-) 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:65
 aligned with DSVD_DESVH | Q46582 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:70
                                    10        20        30        40        50        60        70
            DSVD_DESVH    1 MEEAKQKVVDFLNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGAGK 70
               SCOP domains d1wq2a_ A: aut     omated matches                                      SCOP domains
               CATH domains 1wq2A00 A:1-70      'winged helix' repressor DNA binding domain        CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.-----..eehhhhhh.....hhhhhhhhhhhhhhh..eeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  1wq2 A  1 MEEAKQKVVDFLNS-----SKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGAGK 70
                                    10   |    20        30        40        50        60        70
                                        14    20                                                  


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with DSVD_DESVH | Q46582 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:68
                                    10        20        30        40        50        60        
            DSVD_DESVH    1 MEEAKQKVVDFLNSKSGSKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGA 68
               SCOP domains d1wq2b_ B: auto  mated matches                                       SCOP domains
               CATH domains 1wq2B00 B:1-68   'winged helix' repressor DNA binding domain         CATH domains
           Pfam domains (1) --DsrD-1wq2B01   B:3-68                                              Pfam domains (1)
           Pfam domains (2) --DsrD-1wq2B02   B:3-68                                              Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh..--....eehhhhhhhh...hhhhhhhhhhhhhhh..eeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1wq2 B  1 MEEAKQKVVDFLNSK--SKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLEYWSSGSTTMYGLKGA 68
                                    10    |  |20        30        40        50        60        
                                         15 18
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DsrD] (2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1WQ2)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DSVD_DESVH | Q46582: 1ucr

(-) Related Entries Specified in the PDB File

1ucr X-RAY STRUCTURE OF THE SAME PROTEIN