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- PDB-7z09: Crystal structure of the ground state of bacteriorhodopsin at 1.0... -

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Basic information

Entry
Database: PDB / ID: 7z09
TitleCrystal structure of the ground state of bacteriorhodopsin at 1.05 Angstrom resolution
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / retinal / microbial rhodopsin / ion transport / proton pump / photocycle / ultrahigh resolution
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / 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
EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBorshchevskiy, V. / Kovalev, K. / Round, E. / Efremov, R. / Bourenkov, G. / Gordeliy, V.
Funding support France, Russian Federation, 6items
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 Foundation for Basic Research19-52-15017 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 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,21529
Polymers27,0821
Non-polymers8,13328
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint61 kcal/mol
Surface area11330 Å2
Unit cell
Length a, b, c (Å)60.730, 60.730, 110.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 282.547 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / 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 4 / Detector: CCD / Date: Apr 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.48
ReflectionResolution: 1.05→30.13 Å / Num. obs: 106346 / % possible obs: 99.4 % / Redundancy: 6.255 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Χ2: 0.852 / Net I/σ(I): 9.36 / Num. measured all: 665238 / Scaling rejects: 2324
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
1.05-1.083.7012.9150.5627520784274360.183.38694.8
1.08-1.114.9471.851137856773676530.3932.07398.9
1.11-1.145.1021.1141.6838066747674610.5191.24599.8
1.14-1.175.1830.8282.2237773729472880.6920.92499.9
1.17-1.215.3570.6232.9337717704870410.8170.69299.9
1.21-1.255.4620.445437060678767850.8970.494100
1.25-1.35.5450.3215.4836508658765840.9360.355100
1.3-1.365.650.2596.5635821634663400.9540.28699.9
1.36-1.425.6140.1928.2234159608660850.9710.212100
1.42-1.485.650.14410.1432795580958040.980.15999.9
1.48-1.575.7830.12512.4431946552755240.9880.13899.9
1.57-1.666.6220.15714.5734532521552150.9910.17100
1.66-1.777.5350.15216.137070492149200.9910.163100
1.77-1.928.8490.14718.0340538458245810.9920.156100
1.92-2.110.9170.13521.5246276423942390.9910.141100
2.1-2.3510.810.11924.1641111380338030.990.125100
2.35-2.7110.1980.10425.2134245335833580.9910.11100
2.71-3.328.3160.07224.4223799286228620.9950.077100
3.32-4.76.2020.03722.8213731221622140.9980.04199.9
4.7-30.135.8240.03322.326715122911530.9980.03693.8

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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: 1.05→30.13 Å / Cross valid method: THROUGHOUT / σ(F): 0.92 / Phase error: 24.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1892 3487 3.3 %
Rwork0.1673 102295 -
obs0.1748 105747 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.23 Å2 / Biso mean: 26.1971 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 1.05→30.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 634 88 2507
Biso mean--47.09 45.84 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.070.41321420.4114251439380
1.07-1.090.38381560.33235031518794
1.09-1.110.3231730.32565134530796
1.11-1.130.31391950.30575123531896
1.13-1.160.32411680.30695195536397
1.16-1.180.32831790.30095135531497
1.18-1.210.2781740.29225181535597
1.21-1.240.29651570.28015150530797
1.24-1.280.31851860.27125182536896
1.28-1.320.26321710.25625148531997
1.32-1.370.24481690.24245161533097
1.37-1.430.26061770.22685170534797
1.43-1.490.23261770.21695167534497
1.49-1.570.20371660.20425173533997
1.57-1.670.19171830.18445162534597
1.67-1.80.18311780.18775186536497
1.8-1.980.17891700.17545192536297
1.98-2.260.17961750.15375184535997
2.26-2.850.14351790.1295196537597
2.85-30.130.15991770.12575174535195

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