4B4C | pdb_00004b4c

Crystal structure of the DNA-binding domain of human CHD1.

• PDB DOI: https://doi.org/10.2210/pdb4B4C/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-30 Released: 2012-08-15 
• Deposition Author(s): Allerston, C.K., Cooper, C.D.O., Shrestha, L., Vollmar, M., Burgess-Brown, N., Yue, W.W., Carpenter, E.P., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Gileadi, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: other

Literature

Crystal Structure of the DNA-Binding Domain of Human Chd1.

Allerston, C.K., Cooper, C.D.O., Shrestha, L., Vollmar, M., Burgess-Brown, N., Yue, W.W., Carpenter, E.P., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Gileadi, O.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.33 kDa 
• Atom Count: 1,726 
• Modeled Residue Count: 187 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1	A	211	Homo sapiens	Mutation(s): 0  EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14646 (Homo sapiens) Explore O14646  Go to UniProtKB:  O14646
PHAROS:  O14646 GTEx:  ENSG00000153922

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.464	α = 90
b = 62.464	β = 90
c = 128.085	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
AP_SCALE	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Allerston, C.K., Cooper, C.D.O., Shrestha, L., Vollmar, M., Burgess-Brown, N., Yue, W.W., Carpenter, E.P., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Gileadi, O.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references, Structure summary
• Version 1.2: 2015-03-25
  Changes: Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description