3IHO

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
R-Value Work: 0.182
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 16.61 kDa
Atom Count: 1,158
Modelled Residue Count: 138
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95243
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.290
R-Value Work: 0.182
R-Value Observed: 0.187
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-25

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.