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- PDB-7o8k: NmHR light state structure at 300 us after photoexcitation determ... -

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Basic information

Entry
Database: PDB / ID: 7o8k
TitleNmHR light state structure at 300 us after photoexcitation determined by serial femtosecond crystallography (with extrapolated, dark and light dataset)
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / chloride 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
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / James, D. / Johnson, P. / Weinert, T. / Nass, K. / Furrer, A. / Kekilli, D. ...Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / James, D. / Johnson, P. / Weinert, T. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Bruenle, S. / Casadei, C. / Martiel, I. / Dworkowski, F. / Gashi, D. / Skopintsev, P. / Wranik, M. / Knopp, G. / Panepucci, E. / Panneels, V. / Cirelli, C. / Ozerov, D. / Schertler, G. / Wang, M. / Milne, C. / Standfuss, J. / Schapiro, I. / Heberle, J. / Nogly, P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPZ00P3_174169 Switzerland
CitationJournal: Science / Year: 2022
Title: Dynamics and mechanism of a light-driven chloride pump.
Authors: Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / Weinert, T. / Johnson, P.J.M. / James, D. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Brunle, S. / Casadei, C.M. / Martiel, I. / ...Authors: Mous, S. / Gotthard, G. / Ehrenberg, D. / Sen, S. / Weinert, T. / Johnson, P.J.M. / James, D. / Nass, K. / Furrer, A. / Kekilli, D. / Ma, P. / Brunle, S. / Casadei, C.M. / Martiel, I. / Dworkowski, F. / Gashi, D. / Skopintsev, P. / Wranik, M. / Knopp, G. / Panepucci, E. / Panneels, V. / Cirelli, C. / Ozerov, D. / Schertler, G.F.X. / Wang, M. / Milne, C. / Standfuss, J. / Schapiro, I. / Heberle, J. / Nogly, P.
History
DepositionApr 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3979
Polymers32,9131
Non-polymers2,4848
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint1 kcal/mol
Surface area12080 Å2
Unit cell
Length a, b, c (Å)104.480, 51.180, 78.330
Angle α, β, γ (deg.)90.000, 131.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chloride pumping rhodopsin


Mass: 32913.434 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 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: W8VZW3
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: 50 mM sodium acetate (pH 4.5), 150 mM MgCl2, 100 mM NaCl, 34% PEG400

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→13.5 Å / Num. obs: 55736 / % possible obs: 99.9 % / Redundancy: 136 % / Biso Wilson estimate: 23.37 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.9
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 4354 / CC1/2: 0.4
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
CrystFELv0.8.0data reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
CrystFELv0.8.0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2N

5b2n


Resolution: 1.9→13.45 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 40.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3444 1152 5.16 %
Rwork0.3053 21191 -
obs0.3072 22343 91.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.03 Å2 / Biso mean: 27.9945 Å2 / Biso min: 18.02 Å2
Refinement stepCycle: final / Resolution: 1.9→13.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 161 52 2288
Biso mean--33.25 28.44 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.990.46331360.42962151228776
1.99-2.090.44321380.37682353249182
2.09-2.220.41661610.36842520268188
2.22-2.390.38621590.32922673283293
2.39-2.630.35361350.30942770290596
2.63-3.010.27931380.28092876301498
3.01-3.770.3151390.27132897303699
3.78-13.450.32251460.29422951309799

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