3I3C | pdb_00003i3c

Crystal Structural of CBX5 Chromo Shadow Domain

• PDB DOI: https://doi.org/10.2210/pdb3I3C/pdb

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


• Deposited: 2009-06-30 Released: 2009-08-18 
• Deposition Author(s): Amaya, M.F., Li, Z., Li, Y., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.303 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Literature

Crystal Structural of CBX5 Chromo Shadow Domain

Li, Z., Li, Y., Amaya, M.F., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.86 kDa 
• Atom Count: 1,817 
• Modelled Residue Count: 229 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 5	A, B, C, D	75	Homo sapiens	Mutation(s): 0  Gene Names: CBX5, HP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P45973 (Homo sapiens) Explore P45973  Go to UniProtKB:  P45973
PHAROS:  P45973 GTEx:  ENSG00000094916

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.303 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.66	α = 90
b = 126.587	β = 90
c = 31.399	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Amaya, M.F., Li, Z., Li, Y., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Refinement description