5J70 | pdb_00005j70

The Chd1 DNA-binding domain in complex with 17mer DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb5J70/pdb
• NAKB: 5J70

• Classification: chromatin-binding protein/DNA
• Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-05 Released: 2017-06-21 
• Deposition Author(s): Bowman, G.D., Jenkins, K.R., Hauk, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Chd1 domains communicate across the DNA gyres of the nucleosome

Nodelman, I.M., Jenkins, K.R., Ren, R., Horvath, K.C., Hauk, G., Bowman, G.D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.84 kDa 
• Atom Count: 5,055 
• Modelled Residue Count: 525 
• Deposited Residue Count: 610 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromo domain-containing protein 1	A, B	271	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CHD1, YER164W, SYGP-ORF4 EC: 3.6.4
UniProt
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32657  Go to UniProtKB:  P32657

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*CP*G)-3')	C [auth W], E [auth Y]	17	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP*TP*CP*CP*AP*GP*C)-3')	D [auth X], F [auth Z]	17	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.076	α = 90
b = 57.099	β = 103.9
c = 99.493	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Bowman, G.D., Jenkins, K.R., Hauk, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-R01-084192

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description