3FSP

MutY adenine glycosylase bound to a transition state analog (1N) paired with dG in duplexed DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.202 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural illumination of a mutY glycosylase reaction coordinate intermediate

O'Shea, V.L.Cao, S.Richards, J.L.Horvath, M.P.David, S.S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A/G-specific adenine glycosylase
A
369Geobacillus stearothermophilusGene Names: mutY
EC: 3.2.2.-
Find proteins for P83847 (Geobacillus stearothermophilus)
Go to UniProtKB:  P83847
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'B11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*T*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3'C11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NRI
Query on NRI
C
DNA LINKINGC5 H12 N O5 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.202 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.760α = 90.00
b = 86.141β = 90.00
c = 140.945γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description