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- PDB-8h79: The crystal structure of cyanorhodopsin-II (CyR-II) P7104R from N... -

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Basic information

Entry
Database: PDB / ID: 8h79
TitleThe crystal structure of cyanorhodopsin-II (CyR-II) P7104R from Nodosilinea nodulosa PCC 7104
Componentscyanorhodopsin-II (CyR-II) P7104R
KeywordsMEMBRANE PROTEIN / RETINAL CELL-FREE SYNTHESIS Bacterial type rhodopsin Cyanobacteria
Function / homologyTETRADECANE / HEXANE / N-OCTANE / HEXADECANE / RETINAL
Function and homology information
Biological speciesNodosilinea nodulosa PCC 7104 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K07324 Japan
Japan Society for the Promotion of Science (JSPS)20H05450 Japan
CitationJournal: Isme J / Year: 2024
Title: Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria.
Authors: Hasegawa-Takano, M. / Hosaka, T. / Kojima, K. / Nishimura, Y. / Kurihara, M. / Nakajima, Y. / Ishizuka-Katsura, Y. / Kimura-Someya, T. / Shirouzu, M. / Sudo, Y. / Yoshizawa, S.
History
DepositionOct 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cyanorhodopsin-II (CyR-II) P7104R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,25214
Polymers28,4171
Non-polymers1,83513
Water82946
1
A: cyanorhodopsin-II (CyR-II) P7104R
hetero molecules

A: cyanorhodopsin-II (CyR-II) P7104R
hetero molecules

A: cyanorhodopsin-II (CyR-II) P7104R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,75642
Polymers85,2523
Non-polymers5,50439
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 area15940 Å2
ΔGint-162 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.150, 63.150, 117.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
DetailsThere is no clear evidence that the assembly should be a monomer or trimer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein cyanorhodopsin-II (CyR-II) P7104R


Mass: 28417.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence has been deposited to Genbank with accession number WP_017301364.1
Source: (gene. exp.) Nodosilinea nodulosa PCC 7104 (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 9 types, 59 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#5: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#6: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30
#7: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.8 / Details: 100mM HEPES, 46% PEG 400, 400mM lithium sulfate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→49.6 Å / Num. obs: 17190 / % possible obs: 99.8 % / Redundancy: 12.407 % / Biso Wilson estimate: 27.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.236 / Χ2: 0.97 / Net I/σ(I): 10.25 / Num. measured all: 213269 / Scaling rejects: 495
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
2.07-2.212.3941.6451.835002282528240.6231.716100
2.2-2.3512.5981.1442.6931747252025200.7811.192100
2.35-2.5412.6620.7654.0530427240424030.9070.797100
2.54-2.7812.5260.476.2127444219121910.9650.49100
2.78-3.112.1230.2939.3923871196919690.9840.306100
3.1-3.5911.3210.19613.3420728183118310.9910.205100
3.59-4.3912.7280.08725.0119321151915180.9980.09199.9
4.39-6.2113.2340.07530.516066123212140.9980.07898.5
6.21-49.612.0320.0531.9786637267200.9970.05399.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 2.07→49.6 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1718 10 %
Rwork0.2029 15468 -
obs0.2072 17186 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.47 Å2 / Biso mean: 29.5547 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 2.07→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 125 46 2045
Biso mean--36.5 35.23 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.130.27971380.237812591397100
2.13-2.20.2741420.206812831425100
2.2-2.280.25931380.198212591397100
2.28-2.370.26661440.194612551399100
2.37-2.480.25241400.173712691409100
2.48-2.610.23081420.168612841426100
2.61-2.770.23311440.178612741418100
2.77-2.990.22121470.162712761423100
2.99-3.290.23721450.209412971442100
3.29-3.760.21341400.190412951435100
3.76-4.740.24721460.20851310145699
4.74-49.60.27911520.243214071559100

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