9H44 | pdb_00009h44

Jumonji domain-containing protein 2B with crown ether and crystallization epitope mutations L916G:R917A:A918D

• PDB DOI: https://doi.org/10.2210/pdb9H44/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-17 Released: 2024-12-04 
• Deposition Author(s): Fairhead, M., Strain-Damerell, C., Ye, M., Mackinnon, S.R., Pinkas, D., MacLean, E.M., Koekemoer, L., Damerell, D., Krojer, T., Yue, W., Burgess-Brown, N., Marsden, B., von Delft, F., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 

Starting Model: experimental

Literature

A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants

Fairhead, M., Strain-Damerell, C., Ye, M., Mackinnon, S.R., Pinkas, D., MacLean, E.M., Koekemoer, L., Damerell, D., Krojer, T., Yue, W., Burgess-Brown, N., Marsden, B., von Delft, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.02 kDa 
• Atom Count: 1,211 
• Modeled Residue Count: 128 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4B	A	132	Homo sapiens	Mutation(s): 3  Gene Names: KDM4B, JHDM3B, JMJD2B, KIAA0876 EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for O94953 (Homo sapiens) Explore O94953  Go to UniProtKB:  O94953
PHAROS:  O94953 GTEx:  ENSG00000127663

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O4B	B [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C12 H24 O6 XEZNGIUYQVAUSS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.93	α = 90
b = 87.93	β = 90
c = 142.91	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Fairhead, M., Strain-Damerell, C., Ye, M., Mackinnon, S.R., Pinkas, D., MacLean, E.M., Koekemoer, L., Damerell, D., Krojer, T., Yue, W., Burgess-Brown, N., Marsden, B., von Delft, F., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release