3IHO | pdb_00003iho

The C-terminal glycosylase domain of human MBD4

• PDB DOI: https://doi.org/10.2210/pdb3IHO/pdb

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


• Deposited: 2009-07-30 Released: 2009-08-25 
• Deposition Author(s): Amaya, M.F., Xu, C., Bian, C.B., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.290 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

The C-terminal glycosylase domain of human MBD4

Xu, C., Bian, C.B., Amaya, M.F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., 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: 16.61 kDa 
• Atom Count: 1,158 
• Modeled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 4	A	138	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.290 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.541	α = 90
b = 83.541	β = 90
c = 73.956	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Amaya, M.F., Xu, C., Bian, C.B., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references