7PNC

Dark state structure of Sensory Rhodopsin II solved by serial millisecond crystallography

PDB DOI: https://doi.org/10.2210/pdb7PNC/pdb

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

Deposited: 2021-09-06 Released: 2022-09-14
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: 2.20 Å
R-Value Free: 0.201
R-Value Work: 0.183
R-Value Observed: 0.184

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: 31.5 kDa
Atom Count: 1,999
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPG Query on MPG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A]	G [auth A] J [auth A] K [auth A] L [auth A] M [auth A] G [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth A]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth A]	D [auth A] E [auth A] F [auth A] H [auth A] I [auth A] D [auth A], E [auth A], F [auth A], H [auth A], I [auth A], N [auth A], P [auth A], Q [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A]
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		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 C [auth A] SDF format, chain R [auth A] MOL2 format, chain C [auth A] MOL2 format, chain R [auth A]	C [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain R [auth A] Interactions & Density Focus chain C [auth A] Focus chain R [auth A]