5CHZ | pdb_00005chz

Structure of wild-type human MBD4 bound to a G:T mismatch

• PDB DOI: https://doi.org/10.2210/pdb5CHZ/pdb
• NAKB: 5CHZ

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-07-10 Released: 2016-07-20 
• Deposition Author(s): Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure of wild-type human MBD4 bound to a G:T mismatch

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: 29.81 kDa 
• Atom Count: 1,841 
• Modeled Residue Count: 164 
• Deposited Residue Count: 216 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 4	A	192	Homo sapiens	Mutation(s): 0  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
7-mer DNA	B [auth C]	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
12-mer DNA(G)	C [auth D]	12	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5-mer DNA	D [auth B]	5	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.886	α = 90
b = 54.875	β = 90
c = 104.522	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R21ES023101
Welch Foundation	United States	F-1741

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description