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- PDB-6lm0: The crystal structure of cyanorhodopsin (CyR) N2098R from cyanoba... -

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Basic information

Entry
Database: PDB / ID: 6lm0
TitleThe crystal structure of cyanorhodopsin (CyR) N2098R from cyanobacteria Calothrix sp. NIES-2098
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin Cyanobacteria
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020
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
TETRADECANE / DECANE / HEXANE / N-OCTANE / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesCalothrix sp. NIES-2098 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
CitationJournal: Sci Rep / Year: 2020
Title: A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.
Authors: Hasegawa, M. / Hosaka, T. / Kojima, K. / Nishimura, Y. / Nakajima, Y. / Kimura-Someya, T. / Shirouzu, M. / Sudo, Y. / Yoshizawa, S.
History
DepositionDec 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
C: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,40919
Polymers84,7623
Non-polymers2,64716
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.490, 107.570, 224.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Rhodopsin /


Mass: 28253.928 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calothrix sp. NIES-2098 (bacteria) / Gene: NIES2098_21630 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z4FUT4

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Non-polymers , 6 types, 75 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-C14 / TETRADECANE / Tetradecane


Mass: 198.388 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M sodium acetate (pH5.0), 200mM sodiumu chloride, 39% PEG 500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→49.615 Å / Num. obs: 23218 / % possible obs: 100 % / Redundancy: 72.416 % / Biso Wilson estimate: 45.065 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.727 / Rrim(I) all: 0.732 / Χ2: 1.222 / Net I/σ(I): 10.76 / Num. measured all: 1681366 / Scaling rejects: 446
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.8175.0366.4042276432368536840.6696.443100
2.81-373.6043.562.92253199344034400.7773.582100
3-3.2574.8761.9074.42251059335333530.9111.919100
3.25-3.5672.741.0647.31216765298029800.9621.071100
3.56-3.9868.5550.56612.63186332271827180.9810.57100
3.98-4.5965.6040.35219.29157187239623960.9840.355100
4.59-5.6271.9640.32619.87148030205720570.9860.329100
5.62-7.9576.5180.23623.67125260163716370.9970.237100
7.95-49.61570.4110.16537.42671029619530.9990.16699.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 2.65→49.615 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2741 1988 8.59 %
Rwork0.2275 21167 -
obs0.2315 23155 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.95 Å2 / Biso mean: 41.2469 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.65→49.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 186 59 5791
Biso mean--37.54 40.35 -
Num. residues----709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6501-2.71640.32321400.26341511100
2.7164-2.78980.29331370.23971466100
2.7898-2.87190.2911430.22921487100
2.8719-2.96460.27021430.22211495100
2.9646-3.07050.29771350.21891500100
3.0705-3.19340.30381390.22881485100
3.1934-3.33870.26641480.23491500100
3.3387-3.51470.30231440.23531498100
3.5147-3.73490.27621420.2131503100
3.7349-4.02310.27031390.22581521100
4.0231-4.42770.25461460.21091504100
4.4277-5.06790.24841350.22521530100
5.0679-6.38290.26981490.25411553100
6.3829-49.6150.27171480.2206161499

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