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- PDB-7bmh: Crystal structure of a light-driven proton pump LR (Mac) from Lep... -

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Basic information

Entry
Database: PDB / ID: 7bmh
TitleCrystal structure of a light-driven proton pump LR (Mac) from Leptosphaeria maculans
ComponentsOpsin
KeywordsMEMBRANE PROTEIN / rhodopsin / bacteriorhodopsin / retinal / optogenetics / proton pump / photocycle / eukaryotic rhodopsin / ion transport
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
EICOSANE / OLEIC ACID / Opsin
Similarity search - Component
Biological speciesLeptosphaeria maculans (blackleg of rapeseed fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKovalev, K. / Zabelskii, D. / Dmitrieva, N. / Volkov, O. / Shevchenko, V. / Astashkin, R. / Zinovev, E. / Gordeliy, V.
Funding support Russian Federation, France, 4items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-29-12022 Russian Federation
Russian Foundation for Basic Research17-00-00164 Russian Federation
Ministry of Science and Higher Education of the Russian FederationFSMG -2020-0003 Russian Federation
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02/FA France
CitationJournal: Commun Biol / Year: 2021
Title: Structure-based insights into evolution of rhodopsins.
Authors: Zabelskii, D. / Dmitrieva, N. / Volkov, O. / Shevchenko, V. / Kovalev, K. / Balandin, T. / Soloviov, D. / Astashkin, R. / Zinovev, E. / Alekseev, A. / Round, E. / Polovinkin, V. / Chizhov, I. ...Authors: Zabelskii, D. / Dmitrieva, N. / Volkov, O. / Shevchenko, V. / Kovalev, K. / Balandin, T. / Soloviov, D. / Astashkin, R. / Zinovev, E. / Alekseev, A. / Round, E. / Polovinkin, V. / Chizhov, I. / Rogachev, A. / Okhrimenko, I. / Borshchevskiy, V. / Chupin, V. / Buldt, G. / Yutin, N. / Bamberg, E. / Koonin, E. / Gordeliy, V.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Opsin
B: Opsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78651
Polymers71,9412
Non-polymers13,84449
Water1,838102
1
A: Opsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,03426
Polymers35,9711
Non-polymers7,06325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Opsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75125
Polymers35,9711
Non-polymers6,78124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.540, 70.780, 148.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Opsin / bacteriorhodopsin


Mass: 35970.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptosphaeria maculans (blackleg of rapeseed fungus)
Gene: ops / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q9HGT7
#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM HEPES pH 7.0, 4% PEG 3350, 1 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→49.39 Å / Num. obs: 34762 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.086 / Rrim(I) all: 0.193 / Net I/σ(I): 5.7 / Num. measured all: 168155 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.274.70.9551385429710.8150.4881.0761.499.8
9.07-49.393.90.04722225750.9980.0290.05515.898.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 2.2→19.92 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 1638 4.77 %RANDOM
Rwork0.2361 32702 --
obs0.2384 34340 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.05 Å2 / Biso mean: 36.1578 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 2.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 419 104 4213
Biso mean--44.15 40.59 -
Num. residues----486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.33321290.32722693282299
2.26-2.340.36091270.30012683281099
2.34-2.420.34751380.285526952833100
2.42-2.520.27221320.2682709284199
2.52-2.630.3361400.23972673281399
2.63-2.770.30891280.22592717284599
2.77-2.940.2291210.22542720284199
2.94-3.170.28521470.21522714286199
3.17-3.490.29371390.22362699283899
3.49-3.990.31211330.20852769290299
3.99-5.010.25011470.204527802927100
5.01-19.920.26561570.26472850300798

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