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- PDB-7vgv: Anion free form of light-driven chloride ion-pumping rhodopsin, N... -

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Basic information

Entry
Database: PDB / ID: 7vgv
TitleAnion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / SACLA serial femtosecond crystallography CELL-FREE SYNTHESIS Bacterial type rhodopsin chloride ion pump rhodopsin
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
TETRADECANE / nonane / HEXANE / N-OCTANE / HEXADECANE / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHosaka, T. / Nango, E. / Nakane, T. / Luo, F. / Kimura-Someya, T. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.
Authors: Hosaka, T. / Nomura, T. / Kubo, M. / Nakane, T. / Fangjia, L. / Sekine, S.I. / Ito, T. / Murayama, K. / Ihara, K. / Ehara, H. / Kashiwagi, K. / Katsura, K. / Akasaka, R. / Hisano, T. / ...Authors: Hosaka, T. / Nomura, T. / Kubo, M. / Nakane, T. / Fangjia, L. / Sekine, S.I. / Ito, T. / Murayama, K. / Ihara, K. / Ehara, H. / Kashiwagi, K. / Katsura, K. / Akasaka, R. / Hisano, T. / Tanaka, T. / Tanaka, R. / Arima, T. / Yamashita, A. / Sugahara, M. / Naitow, H. / Matsuura, Y. / Yoshizawa, S. / Tono, K. / Owada, S. / Nureki, O. / Kimura-Someya, T. / Iwata, S. / Nango, E. / Shirouzu, M.
History
DepositionSep 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 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: Chloride pumping rhodopsin
B: Chloride pumping rhodopsin
C: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,69621
Polymers92,1333
Non-polymers2,56318
Water1,26170
1
A: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8498
Polymers30,7111
Non-polymers1,1387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area11470 Å2
MethodPISA
2
B: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6958
Polymers30,7111
Non-polymers9847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-7 kcal/mol
Surface area11450 Å2
MethodPISA
3
C: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1525
Polymers30,7111
Non-polymers4424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-13 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.400, 69.500, 231.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Chloride pumping rhodopsin


Mass: 30710.936 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3

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Non-polymers , 8 types, 88 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H20
#5: Chemical ChemComp-C14 / TETRADECANE


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


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#7: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM HEPES (pH7.0), 400-700 mM K phosphate, and 24-30% PEG400

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.771 Å
DetectorType: MPCCD / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.3→46.3 Å / Num. obs: 50102 / % possible obs: 100 % / Redundancy: 136 % / CC1/2: 0.984 / Net I/σ(I): 5.41
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 2805 / CC1/2: 0.473
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.61data reduction
CrystFEL0.61data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2N

5b2n


Resolution: 2.3→44.46 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2459 4.92 %
Rwork0.2096 47531 -
obs0.2111 49990 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.62 Å2 / Biso mean: 53.833 Å2 / Biso min: 26.77 Å2
Refinement stepCycle: final / Resolution: 2.3→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6193 0 177 70 6440
Biso mean--55.09 59.74 -
Num. residues----791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.340.34351510.296425892740100
2.34-2.390.2861390.28126072746100
2.39-2.440.33921380.270725932731100
2.44-2.50.32821210.255326232744100
2.5-2.560.28481560.238325752731100
2.56-2.630.251190.233926322751100
2.63-2.710.23561430.208925972740100
2.71-2.80.24641460.203225782724100
2.8-2.90.27471310.206426402771100
2.9-3.010.2511140.205926372751100
3.01-3.150.27381240.200526512775100
3.15-3.320.25651460.197326102756100
3.32-3.520.21111190.190926522771100
3.52-3.80.23081590.191926382797100
3.8-4.180.21781150.184926752790100
4.18-4.780.20491660.183826602826100
4.78-6.020.23751350.237527222857100
6.02-44.460.23941370.21612852298999

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