3N0U

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.190 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 

Literature

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

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth A], E [auth B], F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.190 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 
• 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

Entry History 

Deposition Data

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

Revision History  

• 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