1T7P

T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution.

Doublie, S.Tabor, S.Long, A.M.Richardson, C.C.Ellenberger, T.

(1998) Nature 391: 251-258

  • DOI: 10.1038/34593
  • Primary Citation of Related Structures:  
    1T7P

  • PubMed Abstract: 
  • DNA polymerases change their specificity for nucleotide substrates with each catalytic cycle, while achieving error frequencies in the range of 10(-5) to 10(-6). Here we present a 2.2 A crystal structure of the replicative DNA polymerase from bacteriophage T7 complexed with a primer-template and a nucleoside triphosphate in the polymerase active site ...

    DNA polymerases change their specificity for nucleotide substrates with each catalytic cycle, while achieving error frequencies in the range of 10(-5) to 10(-6). Here we present a 2.2 A crystal structure of the replicative DNA polymerase from bacteriophage T7 complexed with a primer-template and a nucleoside triphosphate in the polymerase active site. The structure illustrates how nucleotides are selected in a template-directed manner, and provides a structural basis for a metal-assisted mechanism of phosphoryl transfer by a large group of related polymerases.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed DNA polymeraseA698Escherichia phage T7Mutation(s): 0 
Gene Names: 5
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
Find proteins for P00581 (Escherichia phage T7)
Explore P00581 
Go to UniProtKB:  P00581
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin 1B108Escherichia coli O157:H7Mutation(s): 0 
Gene Names: trxAZ5291ECs4714
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*2DA)-3')P11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*CP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*C)-3')T13N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DG3
      Query on DG3

      Download CCD File 
      P
      2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      HDRRAMINWIWTNU-NTSWFWBYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.279 
      • R-Value Work: 0.240 
      • R-Value Observed: 0.240 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 106.6α = 90
      b = 216.3β = 90
      c = 52.1γ = 90
      Software Package:
      Software NamePurpose
      MLPHAREphasing
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1998-02-25
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2018-04-04
        Changes: Data collection, Database references, Source and taxonomy, Structure summary