4QU2 | pdb_00004qu2

The structure of JMJD7 with alpha-KG

• PDB DOI: https://doi.org/10.2210/pdb4QU2/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-10 Released: 2015-07-15 
• Deposition Author(s): Liu, H.L., Wang, C., Zhang, G.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

The structure of JMJD7 with alpha-KG

Liu, H.L., Wang, C., Dege, C., Ning, F.K., Weisz, J., Hansen, K., Chen, Z.Z., Pan, C.H., Nho, C.W., Nix, J., Marrack, P., Kappler, J., Hagmen, J., Zhang, G.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.6 kDa 
• Atom Count: 5,203 
• Modeled Residue Count: 636 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JmjC domain-containing protein 7	A, B	318	Mus musculus	Mutation(s): 0  Gene Names: Jmjd7 EC: 3.4 (UniProt), 1.14.11.63 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C872 (Mus musculus) Explore P0C872  Go to UniProtKB:  P0C872
IMPC:  MGI:3845785

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	D [auth A], F [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.257 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.535	α = 90
b = 59.516	β = 90
c = 199.583	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-15 
Deposition Author(s): Liu, H.L., Wang, C., Zhang, G.Y.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations