6A57

Structure of histone demethylase REF6 complexed with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*GP*TP*C)-3')B16Arabidopsis thaliana
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*AP*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3')C16Arabidopsis thaliana
Small Molecules
Ligands 2 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.087α = 90.00
b = 96.087β = 90.00
c = 73.905γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL2Mapphasing
HKL-2000data scaling
REFMACrefinement

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