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- PDB-5jrf: Crystal structure of the light-driven sodium pump KR2 bound with ... -

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Basic information

Entry
Database: PDB / ID: 5jrf
TitleCrystal structure of the light-driven sodium pump KR2 bound with iodide ions
ComponentsSodium pumping rhodopsin
KeywordsTRANSPORT PROTEIN / membrane protein / sodium pump / iodide
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
IODIDE ION / EICOSANE / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMelnikov, I. / Polovinkin, V. / Kovalev, K. / Shevchenko, V. / Gushchin, I. / Popov, A. / Gordeliy, V.
CitationJournal: Sci Adv / Year: 2017
Title: Fast iodide-SAD phasing for high-throughput membrane protein structure determination.
Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G. ...Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G.A. / Gordeliy, V. / Popov, A.
History
DepositionMay 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,67729
Polymers32,8791
Non-polymers4,79828
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint29 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.506, 83.749, 234.102
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-431-

HOH

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Components

#1: Protein Sodium pumping rhodopsin


Mass: 32879.008 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-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85 Å / Relative weight: 1
ReflectionResolution: 2.35→60 Å / Num. obs: 26628 / % possible obs: 99.2 % / Redundancy: 6.73 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.25
Reflection shellResolution: 2.35→2.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 1.54 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→117.05 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.833 / SU B: 7.143 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22609 720 5 %RANDOM
Rwork0.18978 ---
obs0.1918 13612 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.5→117.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 89 49 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022242
X-RAY DIFFRACTIONr_bond_other_d0.0030.022189
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9673022
X-RAY DIFFRACTIONr_angle_other_deg1.06534986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96523.67887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46915329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.203154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02558
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9873.7341071
X-RAY DIFFRACTIONr_mcbond_other2.9713.7321070
X-RAY DIFFRACTIONr_mcangle_it4.3295.5981337
X-RAY DIFFRACTIONr_mcangle_other4.3285.61338
X-RAY DIFFRACTIONr_scbond_it3.7324.1821171
X-RAY DIFFRACTIONr_scbond_other3.734.1851172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7396.0941686
X-RAY DIFFRACTIONr_long_range_B_refined7.09943.9992658
X-RAY DIFFRACTIONr_long_range_B_other7.09443.9982657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 47 -
Rwork0.228 989 -
obs--100 %

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