7AVP

Structure of marine actinobacteria clade rhodopsin (MacR) in violet form

PDB DOI: https://doi.org/10.2210/pdb7AVP/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Candidatus Actinomarina minuta
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2020-11-05 Released: 2022-06-01
Deposition Author(s): Gushchin, I., Polovinkin, V., Kovalev, K., Shevchenko, V., Gordeliy, V.
Funding Organization(s): Agence Nationale de la Recherche (ANR), French Infrastructure for Integrated Structural Biology (FRISBI), Grenoble Alliance for Integrated Structural Cell Biology (GRAL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.153
R-Value Work: 0.133
R-Value Observed: 0.134

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Alternating Access Mechanism in a Minimalistic Light-Driven Proton Pump

Shevchenko, V., Gushchin, I., Polovinkin, V., Kovalev, K.

To be published.

Macromolecule Content

Total Structure Weight: 29.63 kDa
Atom Count: 2,161
Modelled Residue Count: 217
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	220	Candidatus Actinomarina minuta	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for S5DM51 (Candidatus Actinomarina minuta) Explore S5DM51 Go to UniProtKB: S5DM51
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S5DM51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [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 N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [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 N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYR Query on LYR	A	L-PEPTIDE LINKING	C₂₆ H₄₂ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.153
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.633	α = 90
b = 40.417	β = 101.37
c = 60.428	γ = 90

Software Package:

Software Name	Purpose
STARANISO	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
REFMAC	refinement
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-19-CE11-0026
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	France	ANR-17-EURE-0003

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 2.0: 2024-10-02
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Structure summary