4O9I | pdb_00004o9i

Structure of CHD4 double chromodomains depicts cooperative folding for DNA binding

PDB DOI: https://doi.org/10.2210/pdb4O9I/pdb

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

Deposited: 2014-01-02 Released: 2015-07-08
Deposition Author(s): Wiggs, K.R., Chruszcz, M., Su, X., Minor, W., Khorasanizadeh, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.264 (Depositor), 0.267 (DCC)
R-Value Work:
0.211 (Depositor), 0.216 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4O9I

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

Literature

Structure of CHD4 double chromodomains depicts cooperative folding for DNA binding

Wiggs, K.R., Chruszcz, M., Su, X., Minor, W., Khorasanizadeh, S.

To be published.

Macromolecule Content

Total Structure Weight: 25 kDa
Atom Count: 1,511
Modeled Residue Count: 176
Deposited Residue Count: 202
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain-helicase-DNA-binding protein 4	A [auth X]	202	Homo sapiens	Mutation(s): 0 Gene Names: CHD4 EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14839 (Homo sapiens) Explore Q14839 Go to UniProtKB: Q14839
PHAROS: Q14839 GTEx: ENSG00000111642
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14839
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth X]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264 (Depositor), 0.267 (DCC)
R-Value Work: 0.211 (Depositor), 0.216 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.211	α = 90
b = 60.475	β = 90
c = 92.988	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SERGUI	data collection
HKL-3000	phasing
SHELXCD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
ARP/wARP	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

Khorasanizadeh, S.

Revision History (Full details and data files)

Version 1.0: 2015-07-08
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-06
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.