5YUW

DNA polymerase IV - DNA ternary complex 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.124 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction

Kottur, J.Nair, D.T.

(2018) Nucleic Acids Res. 46: 5875-5885


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
A, F
352Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dinB (dinP)
EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12))
Go to UniProtKB:  Q47155
Entity ID: 2
MoleculeChainsLengthOrganism
DTN1B,G18Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
DTN2CC,H19Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download SDF File 
Download CCD File 
A, C, F
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.124 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.190α = 90.00
b = 57.010β = 94.59
c = 110.040γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-23 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Kottur, J., Nair, D.T.

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release