2NP6 | pdb_00002np6

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

• PDB DOI: https://doi.org/10.2210/pdb2NP6/pdb
• NAKB: 2NP6

• Classification: TRANSFERASE/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-26 Released: 2007-11-13 
• Deposition Author(s): Lenz, T., Scheidig, A.J., Weinhold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.82 kDa 
• Atom Count: 7,773 
• Modeled Residue Count: 827 
• Deposited Residue Count: 882 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase TaqI	E [auth A], F [auth D]	421	Thermus aquaticus	Mutation(s): 0  Gene Names: taqIM EC: 2.1.1.72
UniProt
Find proteins for P14385 (Thermus aquaticus) Explore P14385  Go to UniProtKB:  P14385

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*TP*CP*GP*(3DR)P*TP*GP*TP*C)-3'	A [auth B], C [auth E]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'	B [auth C], D [auth F]	10	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NEA	I [auth A], K [auth D]	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE C12 H18 N6 O3 S APAPOJUCRZTCHD-WOUKDFQISA-N
GOL	L [auth D], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	G [auth B], H [auth E], J [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.342	α = 90
b = 68.817	β = 92.22
c = 114.196	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Lenz, T., Scheidig, A.J., Weinhold, E.

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description