4E4H | pdb_00004e4h

Crystal structure of Histone Demethylase NO66

• PDB DOI: https://doi.org/10.2210/pdb4E4H/pdb

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


• Deposited: 2012-03-13 Released: 2013-01-30 
• Deposition Author(s): Wu, M., Tao, Y., Zang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

tructural Basis for Tetramerization-dependent Gene Repression by Histone Demethylase NO66

Tao, Y., Wu, M., Sinha, K.M., Zang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 211.11 kDa 
• Atom Count: 15,448 
• Modeled Residue Count: 1,825 
• Deposited Residue Count: 1,852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase NO66	A, B, C, D	463	Homo sapiens	Mutation(s): 0  Gene Names: C14orf169, NO66 EC: 1.14.11.27 (PDB Primary Data), 1.14.11.79 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6W3 (Homo sapiens) Explore Q9H6W3  Go to UniProtKB:  Q9H6W3
PHAROS:  Q9H6W3 GTEx:  ENSG00000170468

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	E [auth A], G [auth B], H [auth C], K [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.352	α = 90
b = 89.352	β = 90
c = 304.863	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Wu, M., Tao, Y., Zang, J.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description