4LG7 | pdb_00004lg7

Crystal structure MBD4 MBD domain in complex with methylated CpG DNA

• PDB DOI: https://doi.org/10.2210/pdb4LG7/pdb
• NAKB: 4LG7

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


• Deposited: 2013-06-27 Released: 2013-07-17 
• Deposition Author(s): Xu, C., Tempel, W., Wernimont, A.K., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.259 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure MBD4 MBD domain in complex with methylated CpG DNA

Xu, C., Tempel, W., Wernimont, A.K., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.18 kDa 
• Atom Count: 983 
• Modeled Residue Count: 87 
• Deposited Residue Count: 92 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 4	A	68	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
DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')	B, C	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.259 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.367	α = 90
b = 78.209	β = 90
c = 40.557	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Xu, C., Tempel, W., Wernimont, A.K., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary