3F2K

Structure of the transposase domain of human Histone-lysine N-methyltransferase SETMAR

• PDB DOI: https://doi.org/10.2210/pdb3F2K/pdb

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


• Deposited: 2008-10-29 Released: 2008-11-25 
• Deposition Author(s): Amaya, M.F., Dombrovski, L., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Botchkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.256 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

The Crystal Structure of Transposase Domain of Human Histone-lysine N-methyltransferase SETMAR.

Dombrovski, L., Amaya, M.F., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Botchkarev, A., Min, J., Plotnikov, A.N., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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: 54.11 kDa 
• Atom Count: 3,535 
• Modelled Residue Count: 384 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETMAR	A, B	226	Homo sapiens	Mutation(s): 0  Gene Names: SETMAR EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H47 (Homo sapiens) Explore Q53H47  Go to UniProtKB:  Q53H47
PHAROS:  Q53H47 GTEx:  ENSG00000170364

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYFA Peptide	C	4	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.256 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.826	α = 90
b = 46.521	β = 92.04
c = 61.748	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Amaya, M.F., Dombrovski, L., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Botchkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection