2OPF

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.240 

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
262Escherichia coli (strain K12)Gene Names: nei
EC: 3.2.2.-, 4.2.99.18
Find proteins for P50465 (Escherichia coli (strain K12))
Go to UniProtKB:  P50465
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3'B12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'C12N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PED
Query on PED
C
NON-POLYMERC5 H13 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.240 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.556α = 90.00
b = 73.556β = 90.00
c = 170.113γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

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: Non-polymer description, Version format compliance