2NP7

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 and pyrrolo-dC at the target base partner position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 

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
Molecule Chains Sequence Length Organism Details
Modification methylase TaqI
A
421 Thermus aquaticus Gene Names: taqIM
EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus)
Go to UniProtKB:  P14385
Entity ID: 1
Molecule Chains Length Organism
5'-D(*GP*TP*TP*CP*GP*(3DR)P*TP*GP*TP*C)-3' B 10 N/A
Entity ID: 2
Molecule Chains Length Organism
5'-D(*GP*AP*CP*AP*(4PC)P*CP*GP*(6MA)P*AP*C)-3' C 10 N/A
Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
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
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
C12 H18 N6 O3 S
APAPOJUCRZTCHD-WOUKDFQISA-N
 Ligand Interaction
Modified Residues  3 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
B
DNA LINKING C5 H11 O6 P

--

4PC
Query on 4PC
C
DNA LINKING C12 H16 N3 O7 P DC
6MA
Query on 6MA
C
DNA LINKING C11 H16 N5 O6 P A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å) Angle (°)
a = 60.210 α = 90.00
b = 70.166 β = 90.00
c = 114.947 γ = 90.00
Software Package:
Software Name Purpose
REFMAC refinement
ProDC data collection
MOLREP phasing
MAR345 data collection
XDS data scaling

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