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- PDB-7o8u: NmHR light state structure at 45 ms (40 - 50 ms) after photoexcit... -

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Basic information

Entry
Database: PDB / ID: 7o8u
TitleNmHR light state structure at 45 ms (40 - 50 ms) after photoexcitation determined by serial millisecond crystallography
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / chloride pump / rhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / plasma membrane / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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)34,7948
Polymers32,9131
Non-polymers1,8807
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-12 kcal/mol
Surface area11610 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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 45 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39 Å / Num. obs: 21052 / % possible obs: 100 % / Redundancy: 721 % / Biso Wilson estimate: 36.86 Å2 / CC1/2: 1 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 2105 / CC1/2: 0.64
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: 2.5→38.96 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3033 493 4.68 %
Rwork0.2513 10042 -
obs0.2537 10535 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.84 Å2 / Biso mean: 41.2181 Å2 / Biso min: 15.6 Å2
Refinement stepCycle: final / Resolution: 2.5→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 122 38 2231
Biso mean--52.58 40.45 -
Num. residues----264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.750.37051060.32782413251993
2.75-3.150.34881290.28972462259197
3.15-3.970.34251260.24752537266398
3.97-38.960.24871320.220626302762100

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