3KTU | pdb_00003ktu

Structure of human 8-oxoGuanine Glycosylase 1 bound to fluorninated oxoG-containing DNA

• PDB DOI: https://doi.org/10.2210/pdb3KTU/pdb
• NAKB: 3KTU

• Classification: HYDROLASE,LYASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-11-26 Released: 2010-07-14 
• Deposition Author(s): Verdine, G.L., Lee, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor) 
• R-Value Work: 
  0.225 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structural investigation of hOGG1 bound to a fluorinated oxoG analog

Verdine, G.L., Lee, S.M.

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)

Macromolecule Content 

• Total Structure Weight: 43.5 kDa 
• Atom Count: 3,069 
• Modeled Residue Count: 339 
• Deposited Residue Count: 342 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A	317	Homo sapiens	Mutation(s): 1  Gene Names: MMH, MUTM, OGG1, OGH1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O15527 (Homo sapiens) Explore O15527  Go to UniProtKB:  O15527
PHAROS:  O15527 GTEx:  ENSG00000114026

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*C)-3')	B	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*CP*AP*(FDG)P*GP*TP*CP*TP*AP*C)-3')	C	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor) 
• R-Value Work:  0.225 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.4	α = 90
b = 92.4	β = 90
c = 212.5	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Verdine, G.L., Lee, S.M.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description