7AVN

Structure of marine actinobacteria clade rhodopsin (MacR) in orange form in P1 space group

PDB DOI: https://doi.org/10.2210/pdb7AVN/pdb

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

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: 1.60 Å
R-Value Free: 0.204
R-Value Work: 0.175
R-Value Observed: 0.177

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

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: 58.57 kDa
Atom Count: 4,017
Modelled Residue Count: 434
Deposited Residue Count: 440
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, B	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLB Query on OLB Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain P [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain P [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain P [auth A]	FA [auth B], P [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain FA [auth B] Focus chain P [auth A] Interactions & Density Focus chain FA [auth B] Focus chain P [auth A]
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	GA [auth B], HA [auth B], Q [auth A], R [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain Q [auth A] Focus chain R [auth A]
LFA Query on LFA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] 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 N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain X [auth B] SDF format, chain C [auth A] SDF format, chain CA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] 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 N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] 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 N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], 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], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] 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 S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] 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 S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.204
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.686	α = 63.66
b = 56.628	β = 78.98
c = 57.386	γ = 80.33

Software Package:

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

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