3W2Y | pdb_00003w2y

Crystal structure of DNA uridine endonuclease Mth212 mutant W205S

PDB DOI: https://doi.org/10.2210/pdb3W2Y/pdb

Classification: HYDROLASE
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-12-06 Released: 2013-12-11
Deposition Author(s): Tabata, N., Shida, T., Arai, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.192 (Depositor), 0.228 (DCC)
R-Value Work:
0.172 (Depositor), 0.209 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of DNA uridine endonuclease Mth212

Tabata, N., Shida, T., Arai, R.

To be published.

Macromolecule Content

Total Structure Weight: 62.06 kDa
Atom Count: 4,751
Modeled Residue Count: 512
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease	A, B [auth D]	260	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 1 Gene Names: MTH212, MTH_212 EC: 3.1.11.2 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for O26314 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26314 Go to UniProtKB: O26314
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26314
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain N [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain N [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain N [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth A], M [auth A], N [auth A], O [auth A], Q [auth D], R [auth D], S [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain C [auth A] MOL2 format, chain P [auth D] MOL2 format, chain C [auth A] mmCIF format, chain P [auth D] mmCIF format, chain C [auth A]	C [auth A], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain P [auth D] Interactions & Density Focus chain C [auth A] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.192 (Depositor), 0.228 (DCC)
R-Value Work: 0.172 (Depositor), 0.209 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.295	α = 90
b = 100.295	β = 90
c = 144.698	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Tabata, N.

Shida, T.

Arai, R.

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description