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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.286 (Depositor), 0.283 (DCC)
R-Value Work:
0.228 (Depositor), 0.227 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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.

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14385
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(GPTPTPCPGP(3DR)PTPGPTPC)-3'	A [auth B], C [auth E]	10	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5'-D(GPAPCPAPTPCPGP(6MA)PAPC)-3'	B [auth C], D [auth F]	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NEA Query on NEA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth D]	I [auth A], K [auth D]	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE C₁₂ H₁₈ N₆ O₃ S APAPOJUCRZTCHD-WOUKDFQISA-N		Interactions Focus chain I [auth A] Focus chain K [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	L [auth D], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain L [auth D] Focus chain M [auth D]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth E] SDF format, chain J [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth E] MOL2 format, chain J [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth E] mmCIF format, chain J [auth A]	G [auth B], H [auth E], J [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth E] Focus chain J [auth A] Interactions & Density Focus chain G [auth B] Focus chain H [auth E] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.286 (Depositor), 0.283 (DCC)
R-Value Work: 0.228 (Depositor), 0.227 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

Lenz, T.

Scheidig, A.J.

Weinhold, E.

Revision History (Full details and data files)

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