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(-) Description

Title :  NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE
 
Authors :  P. Agback, H. Baumann, S. Knapp, R. Ladenstein, T. Hard
Date :  24 Apr 98  (Deposition) - 14 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D
Keywords :  Protein-Dna Interaction, Nonspecific Protein-Dna Interaction, Complex (Dna-Binding Protein/Dna), Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Agback, H. Baumann, S. Knapp, R. Ladenstein, T. Hard
Architecture Of Nonspecific Protein-Dna Interactions In The Sso7D-Dna Complex
Nat. Struct. Biol. V. 5 579 1998
PubMed-ID: 9665172  |  Reference-DOI: 10.1038/836
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)- 3')
    Chains: A, B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA-BINDING PROTEIN 7D
    Atcc: DSM 1616
    Cell Line: BL21
    Chains: C, D
    Collection: DSM 1616
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: SSO7D

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1BBX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BBX)

(-) Sequences/Alignments

NMR Structure
   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:DNA  Length:12
                                           
                  1bbx A  1 CTAGCGCGCTAG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  1bbx B 13 CTAGCGCGCTAG 24
                                    22  


Chain C from PDB  Type:PROTEIN  Length:63
 aligned with DN7D_SULSO | P39476 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:63
                                    11        21        31        41        51        61   
            DN7D_SULSO    2 ATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK 64
               SCOP domains d1bbxc_ C: DNA-binding protein                                  SCOP domains
               CATH domains 1bbxC00 C:1-63  [code=2.40.50.40, no name defined]              CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee.hhh....................................hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  1bbx C  1 ATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK 63
                                    10        20        30        40        50        60   


Chain D from PDB  Type:PROTEIN  Length:63
 aligned with DN7D_SULSO | P39476 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:63
                                    11        21        31        41        51        61   
            DN7D_SULSO    2 ATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK 64
               SCOP domains d1bbxd_ D: DNA-binding protein                                  SCOP domains
               CATH domains 1bbxD00 D:1-63  [code=2.40.50.40, no name defined]              CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee.hhh....................................hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  1bbx D  1 ATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK 63
                                    10        20        30        40        50        60
   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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain C,D   (DN7D_SULSO | P39476)
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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  1bbx
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 Related Entries

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

UniProtKB/Swiss-Prot
        DN7D_SULSO | P39476: 1bnz 1c8c 1jic 5b02 5b03 5b0i 5b0j 5b0k 5b0l 5b0m 5u1c

(-) Related Entries Specified in the PDB File

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