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- PDB-8cl8: Krokinobacter eikastus rhodopsin 2 (KR2) extrapolated map 1us aft... -

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Basic information

Entry
Database: PDB / ID: 8cl8
TitleKrokinobacter eikastus rhodopsin 2 (KR2) extrapolated map 1us after light activation
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: 2.4 Å
AuthorsBertrand, Q. / Kepa, M.W. / Weinert, T. / Wranik, M. / 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 23, 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)37,12927
Polymers29,7811
Non-polymers7,34826
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint89 kcal/mol
Surface area12720 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

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Components

#1: Protein Sodium pumping rhodopsin


Mass: 29780.533 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-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.44 Å3/Da / Density % sol: 64.25 %
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→15.1 Å / Num. obs: 26536 / % possible obs: 60.4 % / Redundancy: 400.15 % / CC1/2: 0.966 / Net I/σ(I): 6.18
Reflection shellResolution: 1.76→1.83 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 172 / CC1/2: 0.315 / % possible all: 3.98
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: 2.4→14.83 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 42.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3583 780 4.96 %
Rwork0.3267 --
obs0.3284 15718 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→14.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 216 62 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072367
X-RAY DIFFRACTIONf_angle_d0.9253134
X-RAY DIFFRACTIONf_dihedral_angle_d15.944879
X-RAY DIFFRACTIONf_chiral_restr0.057335
X-RAY DIFFRACTIONf_plane_restr0.022372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.44221250.41372415X-RAY DIFFRACTION92
2.55-2.750.49511280.38612427X-RAY DIFFRACTION93
2.75-3.020.39711270.35032465X-RAY DIFFRACTION94
3.02-3.450.36071330.31822483X-RAY DIFFRACTION95
3.45-4.330.29951310.28712513X-RAY DIFFRACTION95
4.33-14.830.3181360.30962635X-RAY DIFFRACTION94
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)
11.1586-0.2084-0.22341.32410.26981.6285-0.04480.42110.1125-0.3804-0.09080.1807-0.0688-0.30830.06020.4001-0.0641-0.01910.2980.00550.173557.4154116.9607258.564
21.2516-0.49320.6821.60430.40051.01840.06870.426-0.0048-0.5651-0.03760.072-0.29530.32050.01950.1478-0.1005-0.04770.21570.0490.211466.265111.0542267.932
32.27240.0072-0.00781.4535-0.21692.36950.01990.3078-0.1563-0.4245-0.06090.06090.64750.11270.02380.2635-0.0027-0.00450.1106-0.00440.212263.727101.0724270.376
42.4646-0.02680.42962.21430.29971.774-0.10860.3377-0.2235-0.54930.03920.2216-0.0687-0.31420.16410.1975-0.0494-0.00730.2264-0.01310.161954.4323108.0665265.2342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 228 )
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 271 )

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