Macromolecule Content

Total Structure Weight: 26.95 kDa
Atom Count: 3,406
Modelled Residue Count: 219
Deposited Residue Count: 249
Unique protein chains: 1

7Q88

Light structure of sensory rhodopsin-II solved by serial millisecond crystallography

PDB DOI: https://doi.org/10.2210/pdb7Q88/pdb

Classification: SIGNALING PROTEIN
Organism(s): Natronomonas pharaonis
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2021-11-10 Released: 2023-05-24
Deposition Author(s): Bosman, R., Ortolani, G., Branden, G., Neutze, R.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.250
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of the prolonged photocycle of Sensory Rhodopsin II revealed by serial millisecond crystallography

Bosman, R., Ortolani, G., Branden, G., Neutze, R.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory rhodopsin-2	A	249	Natronomonas pharaonis	Mutation(s): 0 Gene Names: sop2, sopII Membrane Entity: Yes
UniProt
Find proteins for P42196 (Natronomonas pharaonis) Explore P42196 Go to UniProtKB: P42196
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42196
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.250
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.75	α = 90
b = 131.7	β = 90
c = 51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	637295

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.