5T1G | pdb_00005t1g

chromo shadow domain of CBX1 in complex with a histone peptide

• PDB DOI: https://doi.org/10.2210/pdb5T1G/pdb

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


• Deposited: 2016-08-19 Released: 2016-09-14 
• Deposition Author(s): Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

chromo shadow domain of CBX1 in complex with a histone peptide

Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 10.9 kDa 
• Atom Count: 533 
• Modeled Residue Count: 68 
• Deposited Residue Count: 94 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 1	A	79	Homo sapiens	Mutation(s): 0  Gene Names: CBX1, CBX
UniProt & NIH Common Fund Data Resources
Find proteins for P83916 (Homo sapiens) Explore P83916  Go to UniProtKB:  P83916
PHAROS:  P83916 GTEx:  ENSG00000108468

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	B	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AAR	B	L-PEPTIDE LINKING	C6 H16 N5 O		ARG
N7P	B	L-PEPTIDE LINKING	C7 H11 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.243 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35T1G

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.657	α = 90
b = 76.887	β = 90
c = 78.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description