3DLM

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 ?
R-Value Free: 0.237
R-Value Work: 0.208
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15047
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 ?
R-Value Free: 0.237
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.