7D4A | pdb_00007d4a

The Crystal Structure of human JMJD2A Tudor domain from Biortus

• PDB DOI: https://doi.org/10.2210/pdb7D4A/pdb

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


• Deposited: 2020-09-23 Released: 2020-10-07 
• Deposition Author(s): Wang, F., Lv, Z., Cheng, W., Lin, D., Ju, C., Bao, X., Zhu, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of human JMJD2A from Biortus.

Wang, F., Lv, Z., Cheng, W., Lin, D., Ju, C., Bao, X., Zhu, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.14 kDa 
• Atom Count: 955 
• Modeled Residue Count: 116 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A	131	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 1.14.11.66 (PDB Primary Data), 1.14.11.69 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164  Go to UniProtKB:  O75164
PHAROS:  O75164 GTEx:  ENSG00000066135

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: 2.20 Å
• R-Value Free:  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.240 (DCC) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.11	α = 90
b = 135.11	β = 90
c = 135.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Wang, F., Lv, Z., Cheng, W., Lin, D., Ju, C., Bao, X., Zhu, B.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description