3I8Z | pdb_00003i8z

Crystal structure of human chromobox homolog 4 (CBX4)

• PDB DOI: https://doi.org/10.2210/pdb3I8Z/pdb

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


• Deposited: 2009-07-10 Released: 2009-08-25 
• Deposition Author(s): Amaya, M.F., Zhihong, L., Loppnau, P., 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: 1.51 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human chromobox homolog 4 (CBX4)

Zhihong, L., Amaya, M.F., Loppnau, P., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.82 kDa 
• Atom Count: 496 
• Modelled Residue Count: 50 
• Deposited Residue Count: 55 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase CBX4	A	55	Homo sapiens	Mutation(s): 0  Gene Names: CBX4 EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for O00257 (Homo sapiens) Explore O00257  Go to UniProtKB:  O00257
PHAROS:  O00257 GTEx:  ENSG00000141582

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.606	α = 90
b = 58.606	β = 90
c = 32.813	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Amaya, M.F., Zhihong, L., Loppnau, P., 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: 2009-08-25
  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