3DLM | pdb_00003dlm

Crystal structure of Tudor domain of human Histone-lysine N-methyltransferase SETDB1

• PDB DOI: https://doi.org/10.2210/pdb3DLM/pdb

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


• Deposited: 2008-06-27 Released: 2008-08-12 
• Deposition Author(s): Amaya, M.F., Dombrovski, L., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

The crystal structure of Tudor domain of human Histone-lysine N-methyltransferase SETDB1.

Dombrovski, L., Amaya, M.F., Loppnau, P., Bochkarev, A., Min, J., Wu, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.89 kDa 
• Atom Count: 1,914 
• Modeled Residue Count: 208 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	213	Homo sapiens	Mutation(s): 0  Gene Names: SETDB1, KIAA0067, KMT1E EC: 2.1.1.43 (PDB Primary Data), 2.1.1.366 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens) Explore Q15047  Go to UniProtKB:  Q15047
PHAROS:  Q15047 GTEx:  ENSG00000143379

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.518	α = 90
b = 63.689	β = 90
c = 69.083	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Amaya, M.F., Dombrovski, L., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references