6BY9 | pdb_00006by9

Crystal structure of EHMT1

• PDB DOI: https://doi.org/10.2210/pdb6BY9/pdb

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


• Deposited: 2017-12-20 Released: 2018-01-31 
• Deposition Author(s): Dong, A., Wei, Y., Li, A., Tempel, W., Han, S., Sunnerhagen, M., Penn, L., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.238 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of EHMT1

WEI, Y., DONG, A., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., TONG, Y., Structural Genomics Consortium (SGC)

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

Macromolecule Content 

• Total Structure Weight: 35.63 kDa 
• Atom Count: 1,971 
• Modeled Residue Count: 268 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EHMT1	A	328	Homo sapiens	Mutation(s): 0  Gene Names: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.367 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9B1 (Homo sapiens) Explore Q9H9B1  Go to UniProtKB:  Q9H9B1
PHAROS:  Q9H9B1 GTEx:  ENSG00000181090

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A], C [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.238 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36BY9

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.681	α = 90
b = 53.681	β = 90
c = 204.45	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Dong, A., Wei, Y., Li, A., Tempel, W., Han, S., Sunnerhagen, M., Penn, L., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references