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- PDB-7xjc: Crystal structure of bacteriorhodopsin in the ground and K states... -

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Basic information

Entry
Database: PDB / ID: 7xjc
TitleCrystal structure of bacteriorhodopsin in the ground and K states after green laser irradiation
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / proton pump / membrane protein
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / monoatomic ion channel activity / photoreceptor activity / phototransduction / 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
Similarity search - Domain/homology
2,3-DI-PHYTANYL-GLYCEROL / RETINAL / 2,10,23-TRIMETHYL-TETRACOSANE / 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)36,14220
Polymers25,1911
Non-polymers10,95219
Water1,04558
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,42760
Polymers75,5723
Non-polymers32,85557
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 area31720 Å2
ΔGint-255 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 60.570, 110.890
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: 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
#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.: 14 / Source method: obtained synthetically / Formula: C43H88O3
#4: Chemical
ChemComp-SQU / 2,10,23-TRIMETHYL-TETRACOSANE / LIPID FRAGMENT


Mass: 380.734 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H56
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / Details: MO, 2.0-2.5 M Na/K phosphate pH 5.6

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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→50 Å / Num. obs: 52175 / % possible obs: 99.9 % / Redundancy: 5.81 % / Biso Wilson estimate: 23.976 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.082 / Χ2: 0.823 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.33-1.425.5071.1571.3584080.4641.28199.8
1.42-1.515.8380.6932.4479220.7390.762100
1.51-1.635.7050.4094.173680.8710.45100
1.63-1.796.1130.256.9367790.9540.274100
1.79-26.0440.14311.5861380.9840.157100
2-2.315.7180.08318.8354220.9930.092100
2.31-2.835.8170.06425.3145820.9950.0799.8
2.83-3.995.7960.0531.5935620.9970.055100
3.99-505.8740.04634.9819940.9970.05199.8

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Processing

Software
NameVersionClassification
SHELXrefinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zil

5zil


Resolution: 1.33→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1725 -5 %random selection
Rwork0.1306 ---
obs-27207 99.9 %-
Displacement parametersBiso max: 127.8 Å2 / Biso mean: 32.3397 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: LAST / Resolution: 1.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 58 2232

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