6FKE

Structure of 3' phosphatase NExo (D146N) from Neisseria bound to product DNA hairpin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis.

Silhan, J.Zhao, Q.Boura, E.Thomson, H.Forster, A.Tang, C.M.Freemont, P.S.Baldwin, G.S.

(2018) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exodeoxyribonuclease III
A
258Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 1 
Gene Names: xthA
EC: 3.1.11.2
Find proteins for Q9K100 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q9K100
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*A)-3')B15synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.151 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.929α = 90.00
b = 58.929β = 90.00
c = 292.591γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom084369/Z/ 07/Z

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release