4C8D | pdb_00004c8d

Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)

• PDB DOI: https://doi.org/10.2210/pdb4C8D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-30 Released: 2013-10-16 
• Deposition Author(s): Vollmar, M., Johansson, C., Gileadi, C., Goubin, S., Szykowska, A., Krojer, T., Crawley, L., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.239 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Jmjc Domain of Human Histone 3 Lysine-Specific Demethylase 3B (Kdm3B)

Vollmar, M., Johansson, C., Gileadi, C., Goubin, S., Szykowska, A., Krojer, T., Crawley, L., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

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)

Macromolecule Content 

• Total Structure Weight: 40.73 kDa 
• Atom Count: 2,653 
• Modeled Residue Count: 332 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 3B	A	349	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (PDB Primary Data), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7LBC6 (Homo sapiens) Explore Q7LBC6  Go to UniProtKB:  Q7LBC6
PHAROS:  Q7LBC6 GTEx:  ENSG00000120733

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	C [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.239 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.34	α = 90
b = 85.61	β = 90
c = 117.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Vollmar, M., Johansson, C., Gileadi, C., Goubin, S., Szykowska, A., Krojer, T., Crawley, L., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description