2OQ4

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.432 
  • R-Value Work: 0.374 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues

Golan, G.Zharkov, D.O.Grollman, A.P.Shoham, G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Endonuclease VIII
A, B
262Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: nei
Find proteins for P50465 (Escherichia coli (strain K12))
Go to UniProtKB:  P50465
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'C,E13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'D,F13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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B, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PED
Query on PED
D, F
NON-POLYMERC5 H13 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.432 
  • R-Value Work: 0.374 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.130α = 90.00
b = 107.130β = 90.00
c = 164.860γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSphasing
d*TREKdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance