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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.293 (Depositor), 0.293 (DCC)
R-Value Work:
0.233 (Depositor), 0.238 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F6VRB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IR (Subject of Investigation/LOI) Query on IR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	IRIDIUM ION Ir MOHYGSBMXIJZBJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.293 (Depositor), 0.293 (DCC)
R-Value Work: 0.233 (Depositor), 0.238 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.