7AVO

Structure of marine actinobacteria clade rhodopsin (MacR) in orange form in P1211 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin
A, B
220Candidatus Actinomarina minutaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for S5DM51 (Candidatus Actinomarina minuta)
Explore S5DM51 
Go to UniProtKB:  S5DM51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5DM51
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
BA [auth B](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLB
Query on OLB

Download Ideal Coordinates CCD File 
O [auth A](2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
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],
P [auth B],
Q [auth B],
R [auth B],
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYR
Query on LYR
A, B
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.688α = 90
b = 102.009β = 99.75
c = 56.601γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-19-CE11-0026
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-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