2XDP

Crystal structure of the tudor domain of human JMJD2C

• PDB DOI: https://doi.org/10.2210/pdb2XDP/pdb

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


• Deposited: 2010-05-06 Released: 2010-06-09 
• Deposition Author(s): Yue, W.W., Gileadi, C., Krojer, T., Weisbach, H., Ugochukwu, E., Daniel, M., Phillips, C., Chaikuad, A., von Delft, F., Allerston, C., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.206 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Crystal Structure of the Tudor Domain of Human Jmjd2C

Yue, W.W., Gileadi, C., Krojer, T., Weisbach, H., Ugochukwu, E., Daniel, M., Phillips, C., Chaikuad, A., von Delft, F., Allerston, C., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 14.25 kDa 
• Atom Count: 1,155 
• Modelled Residue Count: 119 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4C	A	123	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R0 (Homo sapiens) Explore Q9H3R0  Go to UniProtKB:  Q9H3R0
PHAROS:  Q9H3R0 GTEx:  ENSG00000107077

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.206 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.815	α = 90
b = 79.646	β = 90
c = 81.614	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Yue, W.W., Gileadi, C., Krojer, T., Weisbach, H., Ugochukwu, E., Daniel, M., Phillips, C., Chaikuad, A., von Delft, F., Allerston, C., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description