5ZLV

DNA polymerase IV - DNA ternary complex with 50mM MgCl2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.188 

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
F, A
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
DTN2G,B18Escherichia coli K-12
Entity ID: 3
MoleculeChainsLengthOrganism
DTN1H,C19Escherichia coli K-12
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DPO
Query on DPO

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Download CCD File 
A
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.310α = 90.00
b = 57.240β = 94.74
c = 110.390γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-03-29 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Kottur, J., Nair, D.T.

Revision History 

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