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(-) Description

Title :  CRYSTAL STRUCTURES OF THE HYPERTHERMOPHILIC CHROMOSOMAL PROTEIN SAC7D IN COMPLEX WITH DNA DECAMERS
 
Authors :  T. -P. Ko, H. -M. Chu, C. -Y. Chen, C. -C. Chou, A. H. -J. Wang
Date :  10 May 04  (Deposition) - 03 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Structural Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. P. Ko, H. M. Chu, C. Y. Chen, C. C. Chou, A. H. Wang
Structures Of The Hyperthermophilic Chromosomal Protein Sac7D In Complex With Dna Decamers.
Acta Crystallogr. , Sect. D V. 60 1381 2004
PubMed-ID: 15272160  |  Reference-DOI: 10.1107/S0907444904012065
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'
    Chains: B, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA-BINDING PROTEINS 7A/7B/7D
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS ACIDOCALDARIUS
    Organism Taxid: 2285
    Synonym: SAC7D CHROMOSOMAL PROTEIN, 7 KDA DNA-BINDING PROTEINS A/B/D, SAC7A, SAC7B, SAC7D

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WD1)

(-) Sites  (0, 0)

(no "Site" information available for 1WD1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WD1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WD1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WD1)

(-) Exons   (0, 0)

(no "Exon" information available for 1WD1)

(-) 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:64
 aligned with DN7D_SULAC | P13123 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:64
                                    11        21        31        41        51        61    
           DN7D_SULAC     2 VKVKFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAEREK  65
               SCOP domains d1wd1a_ A: DNA-binding protein                                   SCOP domains
               CATH domains 1wd1A00 A:2-65  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeee...eeeeeee..eeeeeeee..eeeeeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1wd1 A   2 VKVKFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAEREK  65
                                    11        21        31        41        51        61    


Chain B from PDB  Type:DNA  Length:10
                                          
                 1wd1 B 101 CCTACGTAGG 110
                                   110


Chain C from PDB  Type:DNA  Length:10
                                          
                 1wd1 C 111 CCTACGTAGG 120
                                   120
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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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WD1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DN7D_SULAC | P13123)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DN7D_SULAC | P13123: 1azp 1azq 1bf4 1ca5 1ca6 1sap 1wd0 1wto 1wtp 1wtq 1wtr 1wtv 1wtw 1wtx 1wvl 1xx8 1xyi 2xiw 4cj1 4cj2

(-) Related Entries Specified in the PDB File

1azp COMPLEX WITH DNA OCTAMER
1wd0 THE SAME PROTEIN WITH DNA OF CCTATATAGG