3F2K | pdb_00003f2k

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 (Depositor), 0.256 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 54.11 kDa
Atom Count: 3,535
Modeled Residue Count: 384
Deposited Residue Count: 456
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 (PDB Primary Data), 3.1 (UniProt), 2.1.1.357 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H47 (Homo sapiens) Explore Q53H47 Go to UniProtKB: Q53H47
PHAROS: Q53H47 GTEx: ENSG00000170364
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53H47
Sequence Annotations Expand
Reference Sequence

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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	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.256 (DCC)
R-Value Work: 0.205 (Depositor), 0.204 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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
Version 1.4: 2024-10-16
Changes: Structure summary