3KUP | pdb_00003kup

Crystal Structure of the CBX3 Chromo Shadow Domain

• PDB DOI: https://doi.org/10.2210/pdb3KUP/pdb

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


• Deposited: 2009-11-27 Released: 2009-12-08 
• Deposition Author(s): Tempel, W., Li, Z., Li, Y., Kozieradzki, I., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the CBX3 Chromo Shadow Domain

Tempel, W., Li, Z., Li, Y., Kozieradzki, I., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Ouyang, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.91 kDa 
• Atom Count: 1,959 
• Modelled Residue Count: 240 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 3	A, B, C, D	65	Homo sapiens	Mutation(s): 0  Gene Names: CBX3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13185 (Homo sapiens) Explore Q13185  Go to UniProtKB:  Q13185
PHAROS:  Q13185 GTEx:  ENSG00000122565

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	E [auth A], F [auth B], G [auth C], H [auth D], I [auth D], J [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.063	α = 90
b = 75.936	β = 90
c = 85.944	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Tempel, W., Li, Z., Li, Y., Kozieradzki, I., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description