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- PDB-4ov0: Structure of Bacteriorhdopsin Transferred from Amphipol A8-35 to ... -

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Basic information

Entry
Database: PDB / ID: 4ov0
TitleStructure of Bacteriorhdopsin Transferred from Amphipol A8-35 to a Lipidic Mesophase
ComponentsBacteriorhodopsin
KeywordsTRANSPORT PROTEIN / Light-driven proton pump / Retinal attached via Schiff base / Membrane
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
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium sp. (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPolovinkin, V. / Gushchin, I. / Sintsov, M. / Round, E. / Balandin, T. / Chervakov, P. / Schevchenko, V. / Utrobin, P. / Popov, A. / Borshchevskiy, V. ...Polovinkin, V. / Gushchin, I. / Sintsov, M. / Round, E. / Balandin, T. / Chervakov, P. / Schevchenko, V. / Utrobin, P. / Popov, A. / Borshchevskiy, V. / Mishin, A. / Kuklin, A. / Willbold, D. / Popot, J.L. / Gordeliy, V.
CitationJournal: J.Membr.Biol. / Year: 2014
Title: High-resolution structure of a membrane protein transferred from amphipol to a lipidic mesophase.
Authors: Polovinkin, V. / Gushchin, I. / Sintsov, M. / Round, E. / Balandin, T. / Chervakov, P. / Schevchenko, V. / Utrobin, P. / Popov, A. / Borshchevskiy, V. / Mishin, A. / Kuklin, A. / Willbold, D. ...Authors: Polovinkin, V. / Gushchin, I. / Sintsov, M. / Round, E. / Balandin, T. / Chervakov, P. / Schevchenko, V. / Utrobin, P. / Popov, A. / Borshchevskiy, V. / Mishin, A. / Kuklin, A. / Willbold, D. / Chupin, V. / Popot, J.L. / Gordeliy, V.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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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)27,2142
Polymers26,9301
Non-polymers2841
Water25214
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6426
Polymers80,7893
Non-polymers8533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6690 Å2
ΔGint-54 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.999, 60.999, 108.174
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 26929.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium sp. (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Monooleoyl, amphipol A8-35, 1-2M sodium/potassium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→52.83 Å / Num. all: 15434 / Num. obs: 15418 / % possible obs: 99.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→52.826 Å / σ(F): 1.41 / Phase error: 22.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.209 768 4.98 %
Rwork0.1789 --
obs0.1851 15418 99.88 %
all-15434 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→52.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 20 14 1695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081728
X-RAY DIFFRACTIONf_angle_d1.4762362
X-RAY DIFFRACTIONf_dihedral_angle_d17.622585
X-RAY DIFFRACTIONf_chiral_restr0.152278
X-RAY DIFFRACTIONf_plane_restr0.004281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0015-2.15560.24141530.2482910X-RAY DIFFRACTION95
2.1556-2.37150.22311600.20322888X-RAY DIFFRACTION95
2.3715-2.71260.2221630.18322885X-RAY DIFFRACTION95
2.7126-3.40940.19781430.16382944X-RAY DIFFRACTION95
3.4094-14.04560.20711490.17262942X-RAY DIFFRACTION95

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