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- PDB-7z0c: Crystal structure of the K state of bacteriorhodopsin at 1.53 Ang... -

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Basic information

Entry
Database: PDB / ID: 7z0c
TitleCrystal structure of the K state of bacteriorhodopsin at 1.53 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
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: 1.53 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 Foundation19-29-12022 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
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,21529
Polymers27,0821
Non-polymers8,13328
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint61 kcal/mol
Surface area11210 Å2
Unit cell
Length a, b, c (Å)60.990, 60.990, 110.080
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 / Icosane


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 / Oleic acid


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 43.64 %
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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.53→38.11 Å / Num. obs: 30368 / % possible obs: 85 % / Redundancy: 3.059 % / Biso Wilson estimate: 35.473 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.079 / Χ2: 0.971 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
1.84-1.891.3861.5670.3182914875982.15740.2
1.89-1.941.4491.1370.51111414497691.53553.10.22
1.94-21.5330.9620.59143614179371.28866.10.28
2-2.061.6650.7110.951796135910790.93579.40.477
2.06-2.121.8890.4981.512170132811490.64386.50.645
2.12-2.22.2630.4322.222639129011660.54790.40.71
2.2-2.282.7720.3523.053252122711730.43295.60.806
2.28-2.383.5530.343.994218119811870.499.10.869
2.38-2.483.810.2825.154298114311280.32798.70.925
2.48-2.63.8190.2166.894075108610670.25198.30.944
2.6-2.743.8150.1598.953926105210290.18597.80.974
2.74-2.913.8140.12211.6936929919680.14297.70.984
2.91-3.113.8560.08516.4234479178940.09897.50.993
3.11-3.363.8410.06121.6432348668420.07197.20.996
3.36-3.683.8320.03533.5829437957680.04196.60.999
3.68-4.113.8940.02444.3727067246950.028960.999
4.11-4.753.8880.01856.0723256375980.02193.91
4.75-5.823.8870.0225319635355050.02594.40.999
5.82-8.234.0050.02350.9315224233800.02789.80.999
8.23-38.114.0850.01668.658132411990.01882.61

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Processing

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

1c3w


Resolution: 1.53→38.11 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1709 1010 3.4 %
Rwork0.1492 28715 -
obs0.1499 29725 85.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.01 Å2 / Biso mean: 37.1906 Å2 / Biso min: 16.63 Å2
Refinement stepCycle: final / Resolution: 1.53→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 634 89 2504
Biso mean--61.27 51.64 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.610.3865760.36211609168534
1.61-1.710.29641280.26073580370875
1.71-1.840.21851540.2044530468494
1.84-2.030.17971610.16654772493399
2.03-2.320.15671590.14054749490899
2.32-2.930.15121700.12954801497199
2.93-38.110.1591620.13714674483696

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