5FZO | pdb_00005fzo

Crystal structure of the catalytic domain of human JmjD1C

• PDB DOI: https://doi.org/10.2210/pdb5FZO/pdb

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


• Deposited: 2016-03-15 Released: 2016-03-30 
• Deposition Author(s): Nowak, R., Talon, R., Krojer, T., Goubin, S., McDonough, M., Fairhead, M., Oppermann, U., Johansson, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of Human Jmjd1C

Nowak, R., Goubin, S., Mcdonough, M., Fairhead, M., Oppermann, U., Johansson, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.14 kDa 
• Atom Count: 6,004 
• Modelled Residue Count: 678 
• Deposited Residue Count: 704 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C	A	352	Homo sapiens	Mutation(s): 0  EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q15652 (Homo sapiens) Explore Q15652  Go to UniProtKB:  Q15652
PHAROS:  Q15652 GTEx:  ENSG00000171988

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C	B	352	Homo sapiens	Mutation(s): 0  EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q15652 (Homo sapiens) Explore Q15652  Go to UniProtKB:  Q15652
PHAROS:  Q15652 GTEx:  ENSG00000171988

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.32	α = 90
b = 110.92	β = 90
c = 165.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
DIMPLE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Nowak, R., Talon, R., Krojer, T., Goubin, S., McDonough, M., Fairhead, M., Oppermann, U., Johansson, C.

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-04-06
  Changes: Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary