3TED | pdb_00003ted

Crystal structure of the Chd1 DNA-binding domain in complex with a DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb3TED/pdb
• NAKB: 3TED

• Classification: DNA binding protein/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-12 Released: 2011-11-02 
• Deposition Author(s): Sharma, A., Jenkins, K.R., Heroux, A., Bowman, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

DNA-binding domain of Chd1 in complex with a DNA duplex

Sharma, A., Jenkins, K.R., Heroux, A., Bowman, G.D.

(2011) J Biological Chem 

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.83 kDa 
• Atom Count: 2,512 
• Modeled Residue Count: 253 
• Deposited Residue Count: 295 
• 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	271	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CHD1, SYGP-ORF4, YER164W 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
5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3'	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*GP*G)-3'	C	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.67	α = 90
b = 61.426	β = 104.17
c = 76.771	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Sharma, A., Jenkins, K.R., Heroux, A., Bowman, G.D.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description