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- PDB-8rso: Crystal structure of marine actinobacteria clade rhodopsin (MAR) ... -

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Basic information

Entry
Database: PDB / ID: 8rso
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the ground state
ComponentsMicrobial rhodopsin
KeywordsMEMBRANE PROTEIN / Mac / MacR / MAR / proteorhodopsin / PR / xanthorodopsin / XR
Function / homologyEICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / RETINAL
Function and homology information
Biological speciesmarine Actinobacteria clade (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBukhdruker, S. / Kovalev, K. / Astashkin, R. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Sci Adv / Year: 2025
Title: Proteorhodopsin Insights into Molecular Mechanism of Vectorial Proton Transport
Authors: Shevchenko, V. / Gushchin, I. / Polovinkin, V. / Kovalev, K.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microbial rhodopsin
B: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,29833
Polymers48,5542
Non-polymers8,74431
Water2,396133
1
A: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,87621
Polymers24,2771
Non-polymers5,59920
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,42112
Polymers24,2771
Non-polymers3,14411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.710, 55.850, 56.640
Angle α, β, γ (deg.)64.090, 81.520, 85.290
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Microbial rhodopsin


Mass: 24277.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 164 molecules

#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.8 / Details: 3.0 M Ammonium Phosphate buffer, pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.24→47.23 Å / Num. obs: 92902 / % possible obs: 86.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.08 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.037 / Net I/σ(I): 9.6
Reflection shell

Num. unique obs: 4644 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Rpim(I) all% possible all
3.7-47.233.623.70.9940.03198.4
1.24-1.362.51.30.3520.6735.3

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Processing

Software
NameVersionClassification
XDS20220110data reduction
STARANISO2.3.79data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→47.23 Å / SU ML: 0.1092 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.2254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1768 4304 4.63 %
Rwork0.1515 88588 -
obs0.1527 92892 74.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.57 Å2
Refinement stepCycle: LAST / Resolution: 1.25→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 285 133 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023904
X-RAY DIFFRACTIONf_angle_d1.12335240
X-RAY DIFFRACTIONf_chiral_restr0.0776555
X-RAY DIFFRACTIONf_plane_restr0.0089633
X-RAY DIFFRACTIONf_dihedral_angle_d13.77021470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.341610X-RAY DIFFRACTION0.25
1.26-1.270.35730.273156X-RAY DIFFRACTION1.68
1.27-1.290.350150.2673150X-RAY DIFFRACTION3.85
1.29-1.310.283170.2543364X-RAY DIFFRACTION9.22
1.31-1.320.2706420.2466717X-RAY DIFFRACTION18.27
1.32-1.340.3582710.2561315X-RAY DIFFRACTION33.8
1.34-1.360.27931000.23631901X-RAY DIFFRACTION48.04
1.36-1.380.29451140.222399X-RAY DIFFRACTION60.5
1.38-1.40.26611150.21182757X-RAY DIFFRACTION69.12
1.4-1.430.23331450.21633089X-RAY DIFFRACTION79.01
1.43-1.450.28081550.19643483X-RAY DIFFRACTION87.75
1.45-1.480.23041710.17423637X-RAY DIFFRACTION93.01
1.48-1.50.19631500.15963826X-RAY DIFFRACTION94.4
1.5-1.540.20751620.14593741X-RAY DIFFRACTION95.26
1.54-1.570.19881800.1373787X-RAY DIFFRACTION94.93
1.57-1.610.16621720.133773X-RAY DIFFRACTION95.59
1.61-1.650.16851750.1273779X-RAY DIFFRACTION95.58
1.65-1.690.16452180.12183744X-RAY DIFFRACTION95.59
1.69-1.740.16152070.12843762X-RAY DIFFRACTION96.33
1.74-1.80.17842230.13333788X-RAY DIFFRACTION96.26
1.8-1.860.16312060.1263811X-RAY DIFFRACTION96.56
1.86-1.930.17691890.13013813X-RAY DIFFRACTION96.53
1.93-2.020.15452100.12773794X-RAY DIFFRACTION97.07
2.02-2.130.15831780.12363865X-RAY DIFFRACTION97.3
2.13-2.260.16351340.13193904X-RAY DIFFRACTION97.42
2.26-2.440.14251560.13733851X-RAY DIFFRACTION97.83
2.44-2.680.18191840.14963888X-RAY DIFFRACTION98.03
2.68-3.070.18741790.15713884X-RAY DIFFRACTION98.24
3.07-3.870.15652460.16343807X-RAY DIFFRACTION98.18
3.87-47.230.19481970.16913893X-RAY DIFFRACTION98.39

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