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- PDB-9i6i: Room-temperature structure of KR2 rhodopsin in pentameric form at... -

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Basic information

Entry
Database: PDB / ID: 9i6i
TitleRoom-temperature structure of KR2 rhodopsin in pentameric form at 85% relative humidity
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / Sodium pump
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Melo, D. / de Wijn, R. / Bean, R. / Round, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Viscoelastic characterization of the lipid cubic phase provides insights into high-viscosity extrusion injection for XFEL experiments.
Authors: Zabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Letrun, R. / Kim, C. / Sato, T. / Melo, D. / de Wijn, R. / Kharitonov, K. / Smyth, P. / Doerner, K. / Kloos, M. / Dietze, T. / Lopez, ...Authors: Zabelskii, D. / Round, E. / Han, H. / von Stetten, D. / Letrun, R. / Kim, C. / Sato, T. / Melo, D. / de Wijn, R. / Kharitonov, K. / Smyth, P. / Doerner, K. / Kloos, M. / Dietze, T. / Lopez, L. / Bean, R. / Round, A.
History
DepositionJan 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium pumping rhodopsin
B: Sodium pumping rhodopsin
C: Sodium pumping rhodopsin
D: Sodium pumping rhodopsin
E: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,87490
Polymers154,0385
Non-polymers25,83685
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35820 Å2
ΔGint-194 kcal/mol
Surface area43050 Å2
Unit cell
Length a, b, c (Å)136.100, 240.900, 138.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Sodium pumping rhodopsin


Mass: 30807.639 Da / Num. of mol.: 5
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

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Non-polymers , 5 types, 267 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C20H42
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 297 K / Method: lipidic cubic phase / pH: 8 / Details: 3.2M Sodium malonate pH 8.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 297 K / Ambient temp details: Room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→69.25 Å / Num. obs: 45867 / % possible obs: 100 % / Redundancy: 85.1 % / Biso Wilson estimate: 65.93 Å2 / R split: 0.3471 / Net I/σ(I): 2.88
Reflection shellResolution: 3→3.11 Å / Redundancy: 69.6 % / Num. unique obs: 4512 / R split: 1.1592 / % possible all: 100
Serial crystallography measurementPulse energy: 12700 µJ
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: HARE chips

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.1data reduction
CrystFEL0.10.1data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→69.25 Å / SU ML: 0.3156 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.4482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1974 2285 4.98 %
Rwork0.1741 43576 -
obs0.1753 45861 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.23 Å2
Refinement stepCycle: LAST / Resolution: 3→69.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10640 0 1110 182 11932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002511960
X-RAY DIFFRACTIONf_angle_d0.541115879
X-RAY DIFFRACTIONf_chiral_restr0.03811704
X-RAY DIFFRACTIONf_plane_restr0.00441870
X-RAY DIFFRACTIONf_dihedral_angle_d16.70654355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.27171320.22942718X-RAY DIFFRACTION100
3.07-3.140.21481570.1982647X-RAY DIFFRACTION100
3.14-3.210.2491510.20312701X-RAY DIFFRACTION99.89
3.22-3.30.25161300.19142694X-RAY DIFFRACTION99.96
3.3-3.40.20651430.17942694X-RAY DIFFRACTION100
3.4-3.510.23351280.17762706X-RAY DIFFRACTION100
3.51-3.630.1931560.16532704X-RAY DIFFRACTION100
3.63-3.780.18991470.15682687X-RAY DIFFRACTION99.96
3.78-3.950.18461320.15562718X-RAY DIFFRACTION99.96
3.95-4.160.16211400.14682719X-RAY DIFFRACTION100
4.16-4.420.15541540.14322703X-RAY DIFFRACTION100
4.42-4.760.18171420.14982736X-RAY DIFFRACTION100
4.76-5.240.15261400.15912737X-RAY DIFFRACTION100
5.24-60.19881470.18152741X-RAY DIFFRACTION100
6-7.560.21761450.19882787X-RAY DIFFRACTION100
7.56-69.250.23521410.20672884X-RAY DIFFRACTION99.47

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