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

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Basic information

Entry
Database: PDB / ID: 8rss
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the O* state
ComponentsMicrobial rhodopsin
KeywordsMEMBRANE PROTEIN / Mac / MacR / MAR / proteorhodopsin / PR / xanthorodopsin / XR / xanthorhodopsin
Function / homologyEICOSANE / OLEIC ACID / RETINAL
Function and homology information
Biological speciesmarine Actinobacteria clade (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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 the molecular mechanism of vectorial proton transport.
Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / ...Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / Kuklina, D. / Caramello, N. / Rokitskaya, T. / Antonenko, Y. / Rulev, M. / Stoev, C. / Zabelskii, D. / Round, E. / Rogachev, A. / Borshchevskiy, V. / Ghai, R. / Bourenkov, G. / Zeghouf, M. / Cherfils, J. / Engelhard, M. / Chizhov, I. / Rodriguez-Valera, F. / Bamberg, E. / Gordeliy, V.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microbial rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,51716
Polymers24,2771
Non-polymers4,24015
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint19 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.608, 40.174, 60.307
Angle α, β, γ (deg.)90.000, 101.220, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

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Components

#1: Protein Microbial rhodopsin


Mass: 24277.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine Actinobacteria clade (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.4 / Details: 2.6 M Ammonium Phosphate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.41→40.17 Å / Num. obs: 27492 / % possible obs: 88.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 14.12 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.047 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
4.5-40.172.419.713740.9990.01992.4
1.41-1.551.71.313750.7090.34446.5

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Processing

Software
NameVersionClassification
XDS20220110data reduction
STARANISO2.3.94data scaling
PHASER2.8.4phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→40.17 Å / SU ML: 0.1103 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 1347 4.9 %
Rwork0.1594 26139 -
obs0.1612 27486 60.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.08 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 137 147 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282116
X-RAY DIFFRACTIONf_angle_d0.57912852
X-RAY DIFFRACTIONf_chiral_restr0.0558301
X-RAY DIFFRACTIONf_plane_restr0.004352
X-RAY DIFFRACTIONf_dihedral_angle_d13.5717812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.460.179120.1934150X-RAY DIFFRACTION3.39
1.47-1.520.2362350.1643639X-RAY DIFFRACTION14.89
1.52-1.590.2432880.18331483X-RAY DIFFRACTION34.45
1.59-1.680.23421230.17022195X-RAY DIFFRACTION50.93
1.68-1.780.22581250.17182566X-RAY DIFFRACTION59.64
1.78-1.920.22431500.16952932X-RAY DIFFRACTION67.54
1.92-2.110.19621710.15763493X-RAY DIFFRACTION80.28
2.11-2.420.18342200.14574241X-RAY DIFFRACTION96.98
2.42-3.050.18692120.1534218X-RAY DIFFRACTION96.56
3.05-40.170.19622210.16424222X-RAY DIFFRACTION94.43

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