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- PDB-7zn3: Crystal structure of the light-driven inward proton pump xenorhod... -

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Basic information

Entry
Database: PDB / ID: 7zn3
TitleCrystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the L state at pH 8.2 in the presence of sodium at 100K
Componentsxenorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle
Function / homologyEICOSANE / OLEIC ACID / PHOSPHATE ION
Function and homology information
Biological speciesBacillus coahuilensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKovalev, K. / Tsybrov, F. / Alekseev, A. / Bourenkov, G. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Mechanisms of inward transmembrane proton translocation.
Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / ...Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / Chizhov, I. / Royant, A. / Kuzmin, A. / Gushchin, I. / Rosselli, R. / Rodriguez-Valera, F. / Ilyinskiy, N. / Rogachev, A. / Borshchevskiy, V. / Schneider, T.R. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Derived calculations / Category: struct_conn
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: xenorhodopsin
B: xenorhodopsin
C: xenorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,54065
Polymers77,1773
Non-polymers16,36362
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27120 Å2
ΔGint180 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.390, 109.490, 119.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein xenorhodopsin


Mass: 25725.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coahuilensis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 299 molecules

#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.8 M Na/K-Pi pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→49.763 Å / Num. obs: 78671 / % possible obs: 92.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 28.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.9
Reflection shellResolution: 1.6→1.739 Å / Rmerge(I) obs: 2.835 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3935 / CC1/2: 0.389

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIO

1xio


Resolution: 1.6→19.98 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 3851 4.9 %
Rwork0.2034 74663 -
obs0.2041 78514 66.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.41 Å2 / Biso mean: 32.5608 Å2 / Biso min: 16.7 Å2
Refinement stepCycle: final / Resolution: 1.6→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5224 0 612 246 6082
Biso mean--47.25 39.91 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.2299160.313940442010
1.62-1.640.2768140.305648049412
1.64-1.660.4208210.322252554613
1.66-1.680.281300.318457960915
1.68-1.710.3887400.329969773718
1.71-1.730.3259430.312288692922
1.73-1.760.3044560.3181069112527
1.76-1.790.2849700.31031237130731
1.79-1.820.2995810.3121378145935
1.82-1.850.30681030.29511518162139
1.85-1.890.3446880.29411906199447
1.89-1.930.29051210.29142282240357
1.93-1.970.29591290.27882818294770
1.97-2.020.30821650.27093261342681
2.02-2.070.30511720.25153660383291
2.07-2.120.25172110.23193849406096
2.12-2.180.25171910.21543892408397
2.18-2.250.21962140.2023958417298
2.25-2.330.24571710.18653972414398
2.34-2.430.20232140.19023963417799
2.43-2.540.19192180.18523984420299
2.54-2.670.17992030.18373961416499
2.67-2.840.18892090.17383984419398
2.84-3.060.21021990.18694002420198
3.06-3.360.22542090.19154048425799
3.36-3.850.21222280.19414060428899
3.85-4.840.18542130.1944103431699
4.84-19.980.20982220.20834187440997

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