6IP4

Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.

Zheng, S., Hu, H., Ren, H., Yang, Z., Qiu, Q., Qi, W., Liu, X., Chen, X., Cui, X., Li, S., Zhou, B., Sun, D., Cao, X., Du, J.

(2019) Nat Commun 10: 1303-1303


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arabidopsis JMJ13
A
490Arabidopsis thalianaMutation(s): 0 
Gene Names: MQD22.4 (MQD22_4)
Find proteins for F4KIX0 (Arabidopsis thaliana)
Go to UniProtKB:  F4KIX0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
B
12Arabidopsis thalianaMutation(s): 0 
Gene Names: HTR2, HTR3, HTR13, HTR9, HTR1
Find proteins for P59226 (Arabidopsis thaliana)
Go to UniProtKB:  P59226
Small Molecules
Ligands 4 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
SO4
Query on SO4
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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OGA
Query on OGA
Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 128.794α = 90.00
b = 128.794β = 90.00
c = 230.642γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2018-11-02 
  • Released Date: 2019-04-10 
  • Deposition Author(s): Hu, H., Du, J.

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release