2NP6

Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog at the target position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Caught in the act II: Visualization of an intermediate in the DNA base-flipping pathway induced by the adenine-specific DNA methyltransferase M.TaqI

Lenz, T.Scheidig, A.J.Weinhold, E.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Modification methylase TaqI
A, D
421Thermus aquaticusGene Names: taqIM
EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus)
Go to UniProtKB:  P14385
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*TP*CP*GP*(3DR)P*TP*GP*TP*C)-3'B,E10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'C,F10N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NEA
Query on NEA

Download SDF File 
Download CCD File 
A, D
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
C12 H18 N6 O3 S
APAPOJUCRZTCHD-WOUKDFQISA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B, E
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
B, E
DNA LINKINGC5 H11 O6 P

--

6MA
Query on 6MA
C, F
DNA LINKINGC11 H16 N5 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.342α = 90.00
b = 68.817β = 92.22
c = 114.196γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
ProDCdata collection
REFMACrefinement
MAR345data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description