6XAU | pdb_00006xau

Structure of the PR domain from PRDM3

• PDB DOI: https://doi.org/10.2210/pdb6XAU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-04 Released: 2021-06-09 
• Deposition Author(s): Loa, S., Mou, T.C., Sprang, S.R., Briknarova, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Structure of the PR domain from PRDM3

Mou, T.C., Loa, S., Sprang, S.R., Briknarova, K.

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: 13.95 kDa 
• Atom Count: 1,000 
• Modeled Residue Count: 119 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase MECOM	A	123	Mus musculus	Mutation(s): 0  Gene Names: Mecom, Evi1, Mds1, Prdm3 EC: 2.1.1 (PDB Primary Data), 2.1.1.367 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P14404 (Mus musculus) Explore P14404  Go to UniProtKB:  P14404
IMPC:  MGI:95457

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.421	α = 90
b = 44.421	β = 90
c = 147.317	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Loa, S., Mou, T.C., Sprang, S.R., Briknarova, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH P20 GM103546

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2021-06-23
  Changes: Derived calculations, Experimental preparation, Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary