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: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 bacteri ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DNA POLYMERASE)
A
698Enterobacteria phage T7EC: 2.7.7.7, 3.1.11.-
Find proteins for P00581 (Enterobacteria phage T7)
Go to UniProtKB:  P00581
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (THIOREDOXIN)
B
108Escherichia coli (strain K12)Gene Names: trxA (fipA, tsnC)
Find proteins for P0AA25 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA25
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*2DA)-3')P11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DG3
Query on DG3

Download SDF File 
Download CCD File 
P
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2DA
Query on 2DA
P
DNA LINKINGC10 H14 N5 O5 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.600α = 90.00
b = 216.300β = 90.00
c = 52.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-02-25
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance