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- PDB-5vn9: Structure of bacteriorhodopsin from crystals grown at 4 deg C usi... -

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Basic information

Entry
Database: PDB / ID: 5vn9
TitleStructure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / 7TM / retinal protein
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / 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 / 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: 2.594 Å
AuthorsIshchenko, A. / Peng, L. / Zinovev, E. / Vlasov, A. / Lee, S.C. / Kuklin, A. / Mishin, A. / Borshchevskiy, V. / Zhang, Q. / Cherezov, V.
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 1.1Jan 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 1.2Oct 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
Water30617
1
A: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)28,5381
Polymers28,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin


Theoretical massNumber of molelcules
Total (without water)28,5381
Polymers28,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.070, 109.630, 56.560
Angle α, β, γ (deg.)90.00, 116.27, 90.00
Int Tables number4
Space group name H-MP1211

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 277 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 PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.59→28.342 Å / Num. obs: 15034 / % possible obs: 90 % / Redundancy: 2.7 % / Biso Wilson estimate: 46.5 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.3
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1396 / CC1/2: 0.76 / % possible all: 50

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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: 2.594→28.342 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2652 805 5.35 %
Rwork0.2227 --
obs0.2386 15034 88.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.594→28.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 17 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033593
X-RAY DIFFRACTIONf_angle_d0.5834914
X-RAY DIFFRACTIONf_dihedral_angle_d8.0072032
X-RAY DIFFRACTIONf_chiral_restr0.038577
X-RAY DIFFRACTIONf_plane_restr0.003580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5993-2.79970.31911260.27752362X-RAY DIFFRACTION70
2.7997-3.0810.29011590.28232991X-RAY DIFFRACTION89
3.081-3.52580.33071610.24313045X-RAY DIFFRACTION90
3.5258-4.43810.2311610.22012945X-RAY DIFFRACTION88
4.4381-25.03610.28241470.21832911X-RAY DIFFRACTION85

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