6FBU

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 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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

Pomyalov, S.Lansky, S.Golan, G.Zharkov, D.O.Grollman, A.P.Shoham, G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endonuclease 8
A
262Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: nei
Find proteins for P50465 (Escherichia coli (strain K12))
Go to UniProtKB:  P50465
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3')B13synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')C13synthetic construct
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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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 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: 2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.340α = 90.00
b = 75.340β = 90.00
c = 164.380γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
pointlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release