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- PDB-7z0e: Crystal structure of the M state of bacteriorhodopsin at 1.22 Ang... -

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Basic information

Entry
Database: PDB / ID: 7z0e
TitleCrystal structure of the M state of bacteriorhodopsin at 1.22 Angstrom resolution
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / retinal / microbial rhodopsin / ion transport / proton pump / photocycle / ultrahigh resolution
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma 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
2,3-DI-PHYTANYL-GLYCEROL / EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-SQL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsBorshchevskiy, V. / Kovalev, K. / Round, E. / Efremov, R. / Bourenkov, G. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Russian Foundation for Basic Research18-02-40020 Russian Federation
Russian Science Foundation21-64-00018 Russian Federation
Ministry of Science and Higher Education of the Russian Federation075-00958-21-05/730000F.99.1.BV10AA00006 Russian Federation
Ministry of Science and Higher Education of the Russian Federation075-00337-20-03/FSMG-2020-0003 Russian Federation
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins.
Authors: Borshchevskiy, V. / Kovalev, K. / Round, E. / Efremov, R. / Astashkin, R. / Bourenkov, G. / Bratanov, D. / Balandin, T. / Chizhov, I. / Baeken, C. / Gushchin, I. / Kuzmin, A. / Alekseev, A. ...Authors: Borshchevskiy, V. / Kovalev, K. / Round, E. / Efremov, R. / Astashkin, R. / Bourenkov, G. / Bratanov, D. / Balandin, T. / Chizhov, I. / Baeken, C. / Gushchin, I. / Kuzmin, A. / Alekseev, A. / Rogachev, A. / Willbold, D. / Engelhard, M. / Bamberg, E. / Buldt, G. / Gordeliy, V.
History
DepositionFeb 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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

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Assembly

Deposited unit
P: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,87123
Polymers27,0821
Non-polymers6,78922
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint7 kcal/mol
Surface area11390 Å2
Unit cell
Length a, b, c (Å)60.890, 60.890, 109.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules P

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 27081.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945

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Non-polymers , 5 types, 96 molecules

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


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H88O3
#5: Chemical ChemComp-SQL / (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene / squalene / Squalene


Mass: 410.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: Na2HPO4 (5%) and KH2PO4 (95%)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.32
ReflectionResolution: 1.22→30.445 Å / Num. obs: 66766 / % possible obs: 98.1 % / Redundancy: 6.407 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Χ2: 0.963 / Net I/σ(I): 13.75 / Num. measured all: 427782 / Scaling rejects: 118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.22-1.252.2922.2090.449919502843270.1732.77486.1
1.25-1.292.7781.4470.7712683490445650.2461.76693.1
1.29-1.323.4651.1331.1416000477946180.4111.33596.6
1.32-1.364.5311.091.4520622459845510.5151.23499
1.36-1.415.6930.8852.1625522448344830.6970.974100
1.41-1.465.7340.6622.8524815433143280.8120.72899.9
1.46-1.515.7530.4613.9824015417541740.8740.507100
1.51-1.585.7750.3465.2523314403740370.9250.38100
1.58-1.655.7830.2546.9822507389238920.9570.279100
1.65-1.735.8230.1929.0921306365936590.9720.212100
1.73-1.825.8350.14411.620580352735270.9820.158100
1.82-1.935.8260.10215.9219244330333030.9910.112100
1.93-2.068.3990.15921.7226297313131310.9940.168100
2.06-2.2311.9050.13229.6934740291929180.9970.138100
2.23-2.4411.830.09635.0731788268826870.9970.1100
2.44-2.7311.9670.07139.9228995242324230.9980.074100
2.73-3.1511.9030.05347.7225532214521450.9990.055100
3.15-3.8611.1980.0457.3720212180518050.9990.043100
3.86-5.469.1580.0363.3613013142114210.9990.032100
5.46-30.4458.650.02958.766787887720.9990.03298

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.22→30.445 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1951 2161 -
Rwork0.1823 --
obs0.1865 66454 97.68 %
Displacement parametersBiso max: 120.43 Å2 / Biso mean: 28.9432 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: LAST / Resolution: 1.22→30.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 278 74 2151
LS refinement shellResolution: 1.2204→1.2487 Å
RfactorNum. reflection% reflection
Rfree0.4014 --
Rwork0.4262 --
obs-3499 77 %

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