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- PDB-7z0d: Crystal structure of the L state of bacteriorhodopsin at 1.20 Ang... -

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Basic information

Entry
Database: PDB / ID: 7z0d
TitleCrystal structure of the L state of bacteriorhodopsin at 1.20 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: 1.2 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
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 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

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,93328
Polymers27,0821
Non-polymers7,85127
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint63 kcal/mol
Surface area11330 Å2
Unit cell
Length a, b, c (Å)60.920, 60.920, 110.180
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.: 23 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
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 210 / Detector: CCD / Date: Jul 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.2→29.36 Å / Num. obs: 69741 / % possible obs: 96.7 % / Redundancy: 6.205 % / Biso Wilson estimate: 20.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 0.959 / Net I/σ(I): 20.76 / Num. measured all: 432771 / Scaling rejects: 496
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
1.2-1.231.6331.9260.396369529239010.1772.55173.7
1.23-1.261.931.8240.498874520445980.2772.36888.4
1.26-1.32.3941.0810.911581505648380.4121.36295.7
1.3-1.343.0571.0931.1214679489948020.5071.32198
1.34-1.394.0120.9231.6219127478447680.6481.06499.7
1.39-1.435.5230.7222.6125098454545440.8290.797100
1.43-1.495.7370.4893.8325610446744640.8810.53899.9
1.49-1.555.7540.3815.0524575427342710.9340.419100
1.55-1.625.7750.2737.0623549408040780.960.3100
1.62-1.75.8140.1839.8522929394439440.9810.2100
1.7-1.795.8340.13213.0721777373337330.990.145100
1.79-1.95.8560.09816.9520450350234920.9950.10799.7
1.9-2.0310.6350.21528.0635320332533210.9970.22699.9
2.03-2.1911.9810.12543.0736915308130810.9990.131100
2.19-2.411.8810.08953.3733420283128130.9990.09399.4
2.4-2.6812.0060.05767.17311672596259610.06100
2.68-3.111.980.03882.32271952270227010.04100
3.1-3.7911.4630.025103.05219861918191810.027100
3.79-5.379.660.017115.84144131492149210.019100
5.37-29.369.470.017113.43773783681710.01897.7

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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: 1.2→29.36 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 2231 3.27 %
Rwork0.154 66009 -
obs0.1547 68240 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.03 Å2 / Biso mean: 30.8392 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 1.2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 635 98 2518
Biso mean--53.85 45.3 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.230.4429720.42032008208046
1.23-1.250.3531130.40193413352679
1.25-1.290.37491380.3474087422594
1.29-1.320.33331480.32384228437697
1.32-1.360.3141310.29664306443799
1.36-1.40.27311500.236543684518100
1.4-1.450.24051490.199543594508100
1.45-1.510.20491410.16743104451100
1.51-1.580.20721470.151543674514100
1.58-1.660.15521510.134643554506100
1.66-1.770.14861490.126543514500100
1.77-1.90.15831480.132843764524100
1.9-2.10.16811490.133143544503100
2.1-2.40.14011440.127843334477100
2.4-3.020.14241480.127943874535100
3.02-29.360.15421530.140744074560100

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