6LXX | pdb_00006lxx

Frog EPDR1 with an Ir atom

• PDB DOI: https://doi.org/10.2210/pdb6LXX/pdb

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


• Deposited: 2020-02-12 Released: 2021-02-17 
• Deposition Author(s): Park, S., Park, J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

A Single Soaked Iridium (IV) Ion Observed in the Frog Ependymin-Related Protein.

Park, J.K., Park, S.Y.

(2020) Bull Korean Chem Soc 41: 778-781

• DOI: https://doi.org/10.1002/bkcs.12080

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: 23.14 kDa 
• Atom Count: 1,559 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IR (Subject of Investigation/LOI)	C [auth A]	IRIDIUM ION Ir MOHYGSBMXIJZBJ-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.008	α = 90
b = 62.008	β = 90
c = 233.409	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Park, S., Park, J.

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

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-09-01
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary