6L9X | pdb_00006l9x

Xenons in frog EPDR1

• PDB DOI: https://doi.org/10.2210/pdb6L9X/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Xenopus tropicalis
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-11-11 Released: 2020-11-11 
• Deposition Author(s): Park, S.
• Funding Organization(s): National Research Foundation (Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

De novo Phasing Xenons Observed in the Frog Ependymin-Related Protein

Park, S.

(2020) Crystals (Basel) 10: 32-32

• DOI: https://doi.org/10.3390/cryst10010032

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.36 kDa 
• Atom Count: 1,518 
• Modeled Residue Count: 185 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ependymin-related 1	A	196	Xenopus tropicalis	Mutation(s): 0  Gene Names: epdr1
UniProt
Find proteins for F6VRB7 (Xenopus tropicalis) Explore F6VRB7  Go to UniProtKB:  F6VRB7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XE (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.455	α = 90
b = 61.455	β = 90
c = 233.838	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Park, S.

---

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2019R1F1A1059170

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary