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- PDB-8cl7: Krokinobacter eikastus rhodopsin 2 (KR2) in dark state -

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Basic information

Entry
Database: PDB / ID: 8cl7
TitleKrokinobacter eikastus rhodopsin 2 (KR2) in dark state
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / KR2 / Light driven sodium pump / Sodium Pump / Photoactivation / Photocycle
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / RETINAL / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBertrand, Q. / Wranik, M. / Kepa, M.W. / Weinert, T. / Standfuss, J.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.
Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, J.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,39524
Polymers29,8951
Non-polymers6,50023
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint101 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.460, 84.890, 234.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-303-

LFA

21A-437-

HOH

31A-486-

HOH

41A-501-

HOH

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Components

#1: Protein Sodium pumping rhodopsin


Mass: 29894.635 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 BL21(DE3) (bacteria) / Variant (production host): C41 / 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.: 22 / Source method: obtained synthetically / Formula: C20H42
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 200 mM Sodium acetate pH 4.4 150 mM Magnesium Chloride 34 % PEG 200

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.028919 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.028919 Å / Relative weight: 1
ReflectionResolution: 1.76→15.976 Å / Num. obs: 28894 / % possible obs: 65.7 % / Redundancy: 960.89 % / CC1/2: 0.986 / Net I/σ(I): 8.17
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 234.7 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 370 / CC1/2: 0.483
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHASER1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→15.97 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 2000 6.97 %
Rwork0.1553 --
obs0.1573 28709 68.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 109 2416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012429
X-RAY DIFFRACTIONf_angle_d1.1663239
X-RAY DIFFRACTIONf_dihedral_angle_d15.678904
X-RAY DIFFRACTIONf_chiral_restr0.062346
X-RAY DIFFRACTIONf_plane_restr0.011392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.2624230.2379309X-RAY DIFFRACTION11
1.8-1.850.3446340.2477448X-RAY DIFFRACTION17
1.85-1.910.1687460.2189622X-RAY DIFFRACTION23
1.91-1.970.2837620.229834X-RAY DIFFRACTION30
1.97-2.040.2119880.22061164X-RAY DIFFRACTION43
2.04-2.120.23611190.1981588X-RAY DIFFRACTION58
2.12-2.220.24841590.17922136X-RAY DIFFRACTION78
2.22-2.330.22792030.17352701X-RAY DIFFRACTION98
2.33-2.480.18442070.1482760X-RAY DIFFRACTION100
2.48-2.670.17172060.14122760X-RAY DIFFRACTION100
2.67-2.940.14672090.13052791X-RAY DIFFRACTION100
2.94-3.360.1522100.1412808X-RAY DIFFRACTION100
3.36-4.220.16032120.13212837X-RAY DIFFRACTION100
4.22-15.970.20182220.172951X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3452-2.9294-0.68972.348-1.05766.3474-0.0580.5954-0.596-0.4601-0.13280.26690.6561-0.25520.21870.6948-0.08350.00290.418-0.07880.22158.7223105.6621243.2312
21.73590.40440.81583.12111.78215.5775-0.10480.36850.188-0.4991-0.02030.2367-0.5836-0.4880.16820.2289-0.0307-0.0460.24310.03380.193852.9274119.3329260.3858
35.7741-4.46615.96055.7238-4.79616.1803-0.6742-0.19020.2222-0.250.2682-0.2978-0.8544-0.89570.4850.39440.03410.02790.259-0.03870.312156.9868124.5185285.6795
41.43590.17620.49021.43290.48835.8793-0.05860.4406-0.0131-0.46360.0660.0408-0.40070.06650.03810.3024-0.0469-0.03110.20860.01120.18359.5986117.7987257.573
52.9458-0.214-0.4963.4023-3.54663.8734-0.29760.28890.104-0.29340.0121-0.118-0.89761.57990.30720.6729-0.06310.03330.6218-0.02360.21365.4419113.7348245.6884
60.5128-0.19290.92350.9812-1.08667.8715-0.03030.087-0.0782-0.1401-0.0522-0.06220.04610.41740.10350.0947-0.01750.01980.16560.01970.205766.3894110.2772274.5351
71.59710.41460.61581.83792.03445.1928-0.06080.2314-0.1732-0.48340.0662-0.37470.34551.2527-0.2260.34240.09540.09260.3199-0.00440.278771.5273102.8764266.477
82.4796-0.706-1.66731.64391.74184.8753-0.02430.2317-0.4473-0.4129-0.0762-0.11721.0270.11120.18370.45590.02780.04360.177-0.01950.320765.298297.1532271.3945
91.3855-0.0468-1.55381.1288-0.49244.5241-0.12610.0148-0.304-0.21790.04670.21130.6579-0.38050.23880.1795-0.0962-0.00860.16420.04010.244255.055104.0774277.2404
107.59612.52276.69665.06191.15147.5879-0.10981.1054-0.7063-0.7186-0.17840.31540.6470.14080.0870.9878-0.1628-0.02680.5533-0.21020.41654.56596.2839249.8997
112.59090.11551.51522.97611.20384.7773-0.1413-0.0096-0.0026-0.19880.00330.23170.1612-0.52790.22290.1033-0.061-0.00970.13740.01480.196553.9443111.465270.818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 193 )
9X-RAY DIFFRACTION9chain 'A' and (resid 194 through 222 )
10X-RAY DIFFRACTION10chain 'A' and (resid 223 through 236 )
11X-RAY DIFFRACTION11chain 'A' and (resid 237 through 272 )

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