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- PDB-7vgu: Time-resolved serial femtosecond crystallography structure of lig... -

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Basic information

Entry
Database: PDB / ID: 7vgu
TitleTime-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / SACLA serial femtosecond crystallography CELL-FREE SYNTHESIS Bacterial type rhodopsin chloride ion pump rhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / BROMIDE ION / DECANE / HEXANE / RETINAL / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,00712
Polymers30,7111
Non-polymers1,29611
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint13 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.300, 51.100, 78.400
Angle α, β, γ (deg.)90.000, 131.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chloride pumping rhodopsin


Mass: 30710.936 Da / Num. of mol.: 1
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 , 5 types, 66 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 38% PEG400, 300 mM K phosphate, and 100 mM HEPES (pH7.0)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7714 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7714 Å / Relative weight: 1
ReflectionResolution: 2.1→42.8 Å / Num. obs: 18261 / % possible obs: 100 % / Redundancy: 363 % / CC1/2: 0.993 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 929 / CC1/2: 0.918
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2N

5b2n


Resolution: 2.1→29.36 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 899 4.94 %
Rwork0.1821 17305 -
obs0.1835 18204 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.38 Å2 / Biso mean: 32.8699 Å2 / Biso min: 14.98 Å2
Refinement stepCycle: final / Resolution: 2.1→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 97 55 2228
Biso mean--46.18 41.65 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.230.25111400.20862866300699
2.23-2.40.20231630.176728282991100
2.4-2.650.2061610.172728593020100
2.65-3.030.20931410.175229003041100
3.03-3.810.19031430.172128893032100
3.81-29.360.22151510.190829633114100

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