3N0U | pdb_00003n0u

Crystal structure of Tm1821, the 8-oxoguanine DNA glycosylase of Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb3N0U/pdb

Classification: hydrolase, lyase
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-05-14 Released: 2011-04-06
Deposition Author(s): Cooper, D.R., Roy, A., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.190 (Depositor), 0.186 (DCC)
R-Value Work:
0.150 (Depositor), 0.146 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3N0U

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Tm1821, the 8-oxoguanine DNA glycosylase of Thermotoga maritima

Cooper, D.R., Roy, A., Derewenda, Z.S.

To be published.

Macromolecule Content

Total Structure Weight: 77.22 kDa
Atom Count: 5,908
Modeled Residue Count: 626
Deposited Residue Count: 657
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable N-glycosylase/DNA lyase	A, B, C	219	Thermotoga maritima	Mutation(s): 0 Gene Names: ogg, Tm1821, TM_1821 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for Q9X2E1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X2E1 Go to UniProtKB: Q9X2E1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X2E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.190 (Depositor), 0.186 (DCC)
R-Value Work: 0.150 (Depositor), 0.146 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.871	α = 90
b = 93.635	β = 90
c = 135.895	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Derewenda, Z.S.

Integrated Center for Structure and Function Innovation (ISFI)

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.