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- PDB-5vn7: Structure of bacteriorhodopsin from crystals grown at 20 deg Celc... -

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Basic information

Entry
Database: PDB / ID: 5vn7
TitleStructure of bacteriorhodopsin from crystals grown at 20 deg Celcius using GlyNCOC15+4 as an LCP host lipid
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / 7TM / retinal protein
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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsIshchenko, A. / Peng, L. / Zinovev, E. / Vlasov, A. / Lee, S.C. / Kuklin, A. / Mishin, A. / Borshchevskiy, V. / Zhang, Q. / Cherezov, V.
Funding support United States, Russian Federation, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 GM073197 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098538 United States
Ministry of Education and Science of the Russian FederationRFMEFI58716X0026 Russian Federation
CitationJournal: Cryst Growth Des / Year: 2017
Title: Chemically Stable Lipids for Membrane Protein Crystallization.
Authors: Ishchenko, A. / Peng, L. / Zinovev, E. / Vlasov, A. / Lee, S.C. / Kuklin, A. / Mishin, A. / Borshchevskiy, V. / Zhang, Q. / Cherezov, V.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)57,0752
Polymers57,0752
Non-polymers00
Water0
1
A: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)28,5381
Polymers28,5381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)28,5381
Polymers28,5381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.050, 107.050, 149.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 28537.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile)
Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945

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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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 1.9-3.0 M sodium/potassium phosphate buffer (pH5.6), 3.5% v/v methylpentanediol and 0.5% w/v OG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→29.138 Å / Num. obs: 17181 / % possible obs: 97 % / Redundancy: 3 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1716 / CC1/2: 0.476 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XJI

1xji


Resolution: 2.7→28.519 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 846 4.93 %
Rwork0.1962 --
obs0.1976 17176 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→28.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 0 0 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043590
X-RAY DIFFRACTIONf_angle_d0.6464927
X-RAY DIFFRACTIONf_dihedral_angle_d9.8362037
X-RAY DIFFRACTIONf_chiral_restr0.04587
X-RAY DIFFRACTIONf_plane_restr0.004583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.8690.31781390.28192699X-RAY DIFFRACTION96
2.869-3.09030.31221350.26252644X-RAY DIFFRACTION94
3.0903-3.40080.25781450.21622681X-RAY DIFFRACTION97
3.4008-3.89190.19491400.16582770X-RAY DIFFRACTION99
3.8919-4.89930.17311490.16632777X-RAY DIFFRACTION100
4.8993-28.52020.24161380.19662759X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2385-0.5842-0.47631.8945-0.05221.6203-0.0163-0.10090.0860.21150.05820.2325-0.1085-0.1729-0.04250.2726-0.03610.00580.27330.0120.4064-17.0369-3.457-2.6113
21.2445-0.6651.07491.886-1.74221.70850.153-0.1398-0.2091-0.49820.06140.25531.1962-0.4744-0.14680.6767-0.1423-0.04580.35320.05240.4121-16.4946-38.3807-6.1921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 230)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 235)

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