6AB9 | pdb_00006ab9

The crystal structure of the relaxed state of Nonlabens marinus Rhodopsin 3

• PDB DOI: https://doi.org/10.2210/pdb6AB9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Nonlabens marinus S1-08
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2018-07-20 Released: 2019-07-31 
• Deposition Author(s): Yun, J.-H., Ohki, M., Park, J.-H., Jin, Z., Lee, W., Liu, H., Tame, J.R.H., Shibayama, N., Park, S.-Y.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

The pumping mechanism of NM-R3, a light-driven cyanobacterial chloride importer in the rhodopsin family

Yun, J.-H., Ohki, M., Park, J.-H., Jin, Z., Lee, W., Liu, H., Tame, J.R.H., Shibayama, N., Park, S.-Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.25 kDa 
• Atom Count: 2,274 
• Modeled Residue Count: 264 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride pumping rhodopsin	A	296	Nonlabens marinus S1-08	Mutation(s): 0  Gene Names: ClR, NMS_1267 Membrane Entity: Yes
UniProt
Find proteins for W8VZW3 (Nonlabens marinus S1-08) Explore W8VZW3  Go to UniProtKB:  W8VZW3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	D [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
OLA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.634	α = 90
b = 49.22	β = 110.02
c = 69.327	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Yun, J.-H., Ohki, M., Park, J.-H., Jin, Z., Lee, W., Liu, H., Tame, J.R.H., Shibayama, N., Park, S.-Y.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1A2B2008483
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016R1A6A3A04010213

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary