4OFH | pdb_00004ofh

Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis

• PDB DOI: https://doi.org/10.2210/pdb4OFH/pdb
• NAKB: 4OFH

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


• Deposited: 2014-01-14 Released: 2015-04-22 
• Deposition Author(s): Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structure of MBD4 bound to O6MeG:T mispair DNA

Ouzon-Shubeita, H., Lin, Y.-L., Lee, 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)

Macromolecule Content 

• Total Structure Weight: 29.87 kDa 
• Atom Count: 1,782 
• Modeled Residue Count: 165 
• Deposited Residue Count: 216 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 4	A	192	Homo sapiens	Mutation(s): 1  Gene Names: MBD4, MED1 EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O95243 (Homo sapiens) Explore O95243  Go to UniProtKB:  O95243
PHAROS:  O95243 GTEx:  ENSG00000129071

Entity ID: 2
Molecule	Chains	Length	Organism	Image
12-mer DNA(T)	B [auth C]	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
12-mer DNA(O6MeG)	C [auth D]	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.983	α = 90
b = 57.64	β = 90
c = 105.1	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description