8QQO

Continuously illuminated structure of Sensory Rhodopsin II solved by serial millisecond crystallography

PDB DOI: https://doi.org/10.2210/pdb8QQO/pdb
Entry: 8QQO supersedes: 7Q88

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

Deposited: 2023-10-05 Released: 2023-10-18
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: 2.47 Å
R-Value Free: 0.280
R-Value Work: 0.237
R-Value Observed: 0.239

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 26.95 kDa
Atom Count: 3,404
Modelled Residue Count: 219
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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(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
Sequence Annotations 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] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.280
R-Value Work: 0.237
R-Value Observed: 0.239
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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-18

Deposition Author(s):

This entry supersedes: 7Q88

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: 2023-10-18
Type: Initial release
Version 1.1: 2024-10-09
Changes: Structure summary

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.