7Q4N | pdb_00007q4n

transcription factor CDX2 bound to hydroxymethylated DNA

• PDB DOI: https://doi.org/10.2210/pdb7Q4N/pdb
• NAKB: 7Q4N

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


• Deposited: 2021-11-01 Released: 2022-11-16 
• Deposition Author(s): Morgunova, E., Yin, Y., Popov, A., Taipale, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.279 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

transcription factor CDX2 bound to hydroxymethylated DNA

Morgunova, E., Yin, Y., Popov, A., Taipale, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 38.89 kDa 
• Atom Count: 2,634 
• Modeled Residue Count: 201 
• Deposited Residue Count: 206 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein CDX-2	C [auth K], F [auth C]	67	Homo sapiens	Mutation(s): 0  Gene Names: CDX2, CDX3
UniProt & NIH Common Fund Data Resources
Find proteins for Q99626 (Homo sapiens) Explore Q99626  Go to UniProtKB:  Q99626
PHAROS:  Q99626 GTEx:  ENSG00000165556

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (18-MER)	A, D [auth B]	18	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (18-MER)	B [auth D], E	18	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.279 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.897	α = 90
b = 46.634	β = 98.25
c = 120.048	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 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Morgunova, E., Yin, Y., Popov, A., Taipale, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description