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(-) Description

Title :  CRYSTAL STRUCTURES OF PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE (P32)
 
Authors :  P. K. Mandal, G. W. Collie, B. Kauffmann, I. Huc
Date :  28 Mar 16  (Deposition) - 18 May 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Pribnow Box, Consensus Promoter-Sequence, Racemic Dna, Dna Crystallography, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Mandal, G. W. Collie, S. C. Srivastava, B. Kauffmann, I. Huc
Structure Elucidation Of The Pribnow Box Consensus Promoter Sequence By Racemic Dna Crystallography.
Nucleic Acids Res. V. 44 5936 2016
PubMed-ID: 27137886  |  Reference-DOI: 10.1093/NAR/GKW367
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE
    Chains: A, C, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: THIS DODECANUCLEOTIDE SEQUENCE CONTAINS THE PRIBNOW BOX CONSENSUS PROMOTER SEQUENCE TATAAT AT THE CENTRE
    Synthetic: YES
 
Molecule 2 - COMPLEMENTARY SEQUENCE
    Chains: B, D, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1ZN9Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:12binding site for residue ZN A 101
2AC2SOFTWAREDG A:12 , HOH A:203 , HOH A:205 , DG B:24 , HOH B:208binding site for residue ZN A 102
3AC3SOFTWAREDG B:24 , HOH B:201 , HOH B:204 , DC D:15 , HOH D:201binding site for residue ZN B 101
4AC4SOFTWAREDG C:12binding site for residue ZN C 101
5AC5SOFTWAREDG C:12 , DG D:24 , HOH D:212binding site for residue ZN C 102
6AC6SOFTWAREDG D:24 , HOH D:203 , HOH D:204binding site for residue ZN D 101
7AC7SOFTWAREDC B:15 , DG E:12 , HOH E:201 , HOH E:204 , HOH E:206binding site for residue ZN E 101
8AC8SOFTWAREDC C:3 , DG F:24binding site for residue ZN F 101
9AC9SOFTWAREDG E:12 , HOH E:212 , DG F:24 , HOH F:209binding site for residue ZN F 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J0E)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:11
                                          
                  5j0e A  2 GCTATAATGCG 12
                                    11 


Chain B from PDB  Type:DNA  Length:11
                                          
                  5j0e B 14 GCATTATAGCG 24
                                    23 


Chain C from PDB  Type:DNA  Length:11
                                          
                  5j0e C  2 GCTATAATGCG 12
                                    11 


Chain D from PDB  Type:DNA  Length:11
                                          
                  5j0e D 14 GCATTATAGCG 24
                                    23 


Chain E from PDB  Type:DNA  Length:11
                                          
                  5j0e E  2 GCTATAATGCG 12
                                    11 


Chain F from PDB  Type:DNA  Length:11
                                          
                  5j0e F 14 GCATTATAGCG 24
                                    23
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  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 5J0E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J0E)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

5f26 5F26 CONTAINS THE PRIBNOW BOX CONSENSUS SEQUENCE