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- PDB-7xje: Crystal structure of bacteriorhodopsin in the K state refined aga... -

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Basic information

Entry
Database: PDB / ID: 7xje
TitleCrystal structure of bacteriorhodopsin in the K state refined against the extrapolated dataset
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / proton pump / membrane 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
Similarity search - Domain/homology
2,3-DI-PHYTANYL-GLYCEROL / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsTaguchi, S. / Niwa, S. / Takeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Commun Biol / Year: 2023
Title: Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin
Authors: Taguchi, S. / Niwa, S. / Dao, H.A. / Tanaka, Y. / Takeda, R. / Fukai, S. / Hasegawa, K. / Takeda, K.
History
DepositionApr 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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)32,00712
Polymers25,1911
Non-polymers6,81611
Water41423
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,02036
Polymers75,5723
Non-polymers20,44833
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_635-y+1,x-y-2,z1
crystal symmetry operation3_865-x+y+3,-x+1,z1
Buried area23990 Å2
ΔGint-212 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 60.570, 110.880
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: 25190.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum NRC-1 (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C43H88O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: MO, 2.0-2.5 M PHOSPHATE

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Data collection

DiffractionMean temperature: 15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.33→20 Å / Num. obs: 290824 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.99 / Net I/σ(I): 10.08
Reflection shellResolution: 1.33→1.4 Å / Mean I/σ(I) obs: 1.24 / Num. unique obs: 44229 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.27data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1300028945

Resolution: 1.33→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.293 2436 -
Rwork0.274 --
obs-49716 100 %
Displacement parametersBiso max: 147.98 Å2 / Biso mean: 31.6958 Å2 / Biso min: 9.47 Å2
Refinement stepCycle: LAST / Resolution: 1.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 240 23 2042

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