6A59

Structure of histone demethylase REF6 at 1.8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 6A58 - determined by Tian, Z., Chen, Z.  
  • 6A57 - determined by Tian, Z., Chen, Z.  

Literature

Structure of histone demethylase REF6 complexed with DNA

Tian, Z.Chen, Z.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase REF6
A
140Arabidopsis thalianaMutation(s): 0 
Gene Names: REF6 (JMJ12, PKDM9A)
EC: 1.14.11.-
Find proteins for Q9STM3 (Arabidopsis thaliana)
Go to UniProtKB:  Q9STM3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.215 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 63.445α = 90.00
b = 63.445β = 90.00
c = 43.533γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
HKL2Mapphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-22 
  • Released Date: 2019-06-26 
  • Deposition Author(s): Tian, Z., Chen, Z.

Funding OrganizationLocationGrant Number
National Basic Research Program of China(973 Program)China2016YFC1200400

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release