3IH7 | pdb_00003ih7

Crystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA

• PDB DOI: https://doi.org/10.2210/pdb3IH7/pdb
• NAKB: 3IH7

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


• Deposited: 2009-07-29 Released: 2010-11-03 
• Deposition Author(s): Verdine, G.L., Crenshaw, C.M., Oo, K.S., Kutchukian, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.267 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

A Catalytic Checkpoint in Base Excision by the Human 8-Oxoguanine DNA Glycosylase hOGG1

Crenshaw, C.M., Oo, K.S., Kutchukian, P.S., Verdine, G.L.

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: 43.95 kDa 
• Atom Count: 3,023 
• Modeled Residue Count: 339 
• Deposited Residue Count: 343 
• 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	316	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
5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'	B	14	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(AP*TP*CP*TP*GP*GP*AP*CP*CP*TP*GP*CP*A)-3'	C	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.267 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91	α = 90
b = 91	β = 90
c = 211.6	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Verdine, G.L., Crenshaw, C.M., Oo, K.S., Kutchukian, P.S.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description