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- PDB-7z0a: Crystal structure of the ground state of bacteriorhodopsin at 1.2... -

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Basic information

Entry
Database: PDB / ID: 7z0a
TitleCrystal structure of the ground 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


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: 1.22 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 area11310 Å2
Unit cell
Length a, b, c (Å)60.970, 60.970, 109.560
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: 43.33 %
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: 0.9334 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.22→29.37 Å / Num. obs: 63006 / % possible obs: 91.2 % / Redundancy: 6.775 % / Biso Wilson estimate: 22.615 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.043 / Χ2: 1.001 / Net I/σ(I): 24.64 / Num. measured all: 426846 / Scaling rejects: 199
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
1.22-1.251.3952.5090.33011508821590.153.48242.4
1.25-1.281.5871.5650.455014493731600.2082.13964
1.28-1.321.841.2490.667285484639590.3161.66581.7
1.32-1.362.2291.0680.879771470143830.3641.37893.2
1.36-1.42.8340.8241.2912664456544690.5441.01697.9
1.4-1.453.7430.6232.116430440743900.7290.72999.6
1.45-1.515.2590.53.3722265423542340.860.556100
1.51-1.576.2090.4354.925445409940980.9310.474100
1.57-1.646.8950.4046.7927056392439240.9590.436100
1.64-1.727.5870.3229.5228230372137210.9790.345100
1.72-1.818.450.25812.8630183357235720.9880.275100
1.81-1.929.5280.18618.9932263338733860.9950.196100
1.92-2.0611.7310.12630.8537339318331830.9980.131100
2.06-2.2212.0130.07347.8435341294229420.9990.076100
2.22-2.4312.1920.04962.92333212733273310.051100
2.43-2.7212.2380.03674.87300562456245610.037100
2.72-3.1412.2120.02793.25266582183218310.028100
3.14-3.8511.9090.018122.46219721845184510.019100
3.85-5.4410.4650.014137.11150171435143510.015100
5.44-29.379.7220.014130.87752579877410.01697

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.22→29.37 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.167 2029 3.26 %
Rwork0.1403 60204 -
obs0.1412 62233 90.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.38 Å2 / Biso mean: 33.6222 Å2 / Biso min: 12.89 Å2
Refinement stepCycle: final / Resolution: 1.22→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 634 88 2507
Biso mean--57.22 48.59 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.22-1.250.4542470.40711397144429
1.25-1.280.3663940.37232896299061
1.28-1.320.37061290.33113838396781
1.32-1.360.33061440.30894421456593
1.36-1.410.30451580.26994692485098
1.41-1.470.2431620.201647354897100
1.47-1.530.19431600.155647574917100
1.53-1.610.16991600.138447974957100
1.61-1.710.16021630.118747484911100
1.71-1.850.16181610.114747704931100
1.85-2.030.14461620.11447964958100
2.03-2.330.14121600.114647494909100
2.33-2.930.12711660.119348054971100
2.93-29.370.16091630.134248034966100

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