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- PDB-6tk6: Femtosecond to millisecond structural changes in a light-driven s... -

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Basic information

Entry
Database: PDB / ID: 6tk6
TitleFemtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in neutral conditions with attached light datasets at 800fs, 2ps, 100ps, 1ns, 16ns, 1us, 30us, 150us, 1ms and 20ms
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / Sodium pumping rhodopsin / time-resolved / serial femtosecond crystallograpy / room-temperature
Function / homology
Function and homology information


Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
EICOSANE / RETINAL / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSkopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R. / Johnson, P. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. ...Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R. / Johnson, P. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. / Nass, K. / Knopp, G. / Cirelli, C. / Gashi, D. / Mous, S. / Wranik, M. / Gruhl, T. / Kekilli, D. / Bruenle, S. / Deupi, X. / Schertler, G.F.X. / Benoit, R. / Panneels, V. / Nogly, P. / Schapiro, I. / Milne, C. / Heberle, J. / Standfuss, J.
Funding support Switzerland, Germany, Israel, 9items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_141235 Switzerland
Swiss National Science Foundation31003A_159558 Switzerland
Swiss National Science FoundationPZ00P3_174169 Switzerland
German Research FoundationSFB-1078, project B3 Germany
German Research FoundationSPP-1926, HE 2063/6-1 Germany
European Research CouncilMarie-Sklodowska-Curie No 701646 Switzerland
European Research CouncilMarie-Sklodowska-Curie No 701647 Switzerland
European Research Council678169 Israel
German Research FoundationSFB 1078 Protonation Dynamics in Protein Function Mercator fellowship Israel
CitationJournal: Nature / Year: 2020
Title: Femtosecond-to-millisecond structural changes in a light-driven sodium pump.
Authors: Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R.K. / Johnson, P.J.M. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. / Nass, K. / Knopp, G. / Cirelli, C. / Arrell, ...Authors: Skopintsev, P. / Ehrenberg, D. / Weinert, T. / James, D. / Kar, R.K. / Johnson, P.J.M. / Ozerov, D. / Furrer, A. / Martiel, I. / Dworkowski, F. / Nass, K. / Knopp, G. / Cirelli, C. / Arrell, C. / Gashi, D. / Mous, S. / Wranik, M. / Gruhl, T. / Kekilli, D. / Brunle, S. / Deupi, X. / Schertler, G.F.X. / Benoit, R.M. / Panneels, V. / Nogly, P. / Schapiro, I. / Milne, C. / Heberle, J. / Standfuss, J.
History
DepositionNov 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,52628
Polymers32,8951
Non-polymers7,63127
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint126 kcal/mol
Surface area11520 Å2
Unit cell
Length a, b, c (Å)41.540, 84.480, 235.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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Components

#1: Protein Sodium pumping rhodopsin


Mass: 32894.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dokdonia eikasta (bacteria) / Gene: NaR / Production host: Escherichia coli (E. coli) / References: UniProt: N0DKS8
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C20H42
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.4
Details: 200 mM Sodium Acetate pH 4.4, 150 mM MgCl2, 35% PEG 200

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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: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→12.43 Å / Num. obs: 31741 / % possible obs: 77.2 % / Redundancy: 1328 % / CC1/2: 1 / R split: 0.049 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→2.3 Å / Redundancy: 872 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 12867 / CC1/2: 0.95 / R split: 0.3 / % possible all: 35.4
Serial crystallography measurementFocal spot size: 3.5 µm2 / Pulse photon energy: 12.4 keV / XFEL pulse repetition rate: 50 Hz
Serial crystallography sample deliveryDescription: High viscosity injector / Method: injection
Serial crystallography sample delivery injectionInjector nozzle: capillary / Jet diameter: 75 µm

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3x3c

3x3c


Resolution: 1.6→12.426 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 2077 6.55 %
Rwork0.1879 29651 -
obs0.1898 31728 57.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.72 Å2 / Biso mean: 39.2853 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: final / Resolution: 1.6→12.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 242 60 2385
Biso mean--62.42 46.13 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6001-1.63720.4794220.32211816
1.6372-1.67810.3451120.29852517
1.6781-1.72340.3501250.306133510
1.7234-1.77390.3288410.318747914
1.7739-1.8310.3512470.268767220
1.831-1.89620.3375640.26594027
1.8962-1.97190.3209920.2355126737
1.9719-2.06120.27581290.2464184354
2.0612-2.16940.25421900.2417276381
2.1694-2.30450.24962350.23338698
2.3045-2.48110.24372400.20583436100
2.4811-2.72840.22352400.19523452100
2.7284-3.11770.23022420.1933482100
3.1177-3.90760.17952450.16733514100
3.9076-12.4260.20492530.17123650100

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