6XAZ | pdb_00006xaz

Structure of the PR domain from human PRDM5

• PDB DOI: https://doi.org/10.2210/pdb6XAZ/pdb

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


• Deposited: 2020-06-05 Released: 2021-06-09 
• Deposition Author(s): Mou, T.C., Kerchner, K.M., 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: 1.70 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

Structure of the PR domain from human PRDM5

Mou, T.C., Kerchner, K.M., 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.17 kDa 
• Atom Count: 2,146 
• Modeled Residue Count: 243 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain zinc finger protein 5	A, B	130	Homo sapiens	Mutation(s): 0  Gene Names: PRDM5, PFM2 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQX1 (Homo sapiens) Explore Q9NQX1  Go to UniProtKB:  Q9NQX1
PHAROS:  Q9NQX1 GTEx:  ENSG00000138738

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth B], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.527	α = 90
b = 56.083	β = 90
c = 105.307	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Mou, T.C., Kerchner, K.M., 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
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description