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- PDB-7q36: Crystal structure of KR2 sodium pump rhodopsin pressurized with k... -

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Basic information

Entry
Database: PDB / ID: 7q36
TitleCrystal structure of KR2 sodium pump rhodopsin pressurized with krypton
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / sodium pump
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / HEXANE / KRYPTON / EICOSANE / RETINAL / Sodium pumping rhodopsin
Function and homology information
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMelnikov, I. / Rulev, M. / Astashkin, R. / Kovalev, K. / Carpentier, P. / Gordeliy, V. / Popov, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action.
Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / ...Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / Mueller-Dieckmann, C. / van der Linden, P. / Carpentier, P. / Leonard, G. / Gordeliy, V. / Popov, A.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)39,69942
Polymers31,5401
Non-polymers8,15941
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint106 kcal/mol
Surface area11790 Å2
Unit cell
Length a, b, c (Å)40.489, 82.180, 233.442
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-333-

KR

21A-335-

KR

31A-411-

HOH

41A-426-

HOH

51A-453-

HOH

61A-481-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium pumping rhodopsin


Mass: 31540.439 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) / Strain (production host): BL21(DE3) / References: UniProt: N0DKS8

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Non-polymers , 6 types, 122 molecules

#2: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 2.0 M sodium malonate, pH 4.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8637 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8637 Å / Relative weight: 1
ReflectionResolution: 2.6→116.72 Å / Num. obs: 23274 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.192 / Net I/σ(I): 9.29
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 7 % / Rmerge(I) obs: 2 / Num. unique obs: 4905 / CC1/2: 0.4 / Rrim(I) all: 2.117 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTL

4xtl


Resolution: 2.6→116.72 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.838 / SU B: 11.623 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.615 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26904 607 4.9 %RANDOM
Rwork0.21647 ---
obs0.21902 11896 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å20 Å2-0 Å2
2---0.23 Å20 Å2
3----3.69 Å2
Refinement stepCycle: 1 / Resolution: 2.6→116.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 206 81 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132382
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172420
X-RAY DIFFRACTIONr_angle_refined_deg1.141.6433154
X-RAY DIFFRACTIONr_angle_other_deg1.0691.5445552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36322.3100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58815338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.913154
X-RAY DIFFRACTIONr_chiral_restr0.0470.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
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_it1.945.0421087
X-RAY DIFFRACTIONr_mcbond_other1.9365.0381086
X-RAY DIFFRACTIONr_mcangle_it3.1497.5621357
X-RAY DIFFRACTIONr_mcangle_other3.1487.5681358
X-RAY DIFFRACTIONr_scbond_it2.0425.5191295
X-RAY DIFFRACTIONr_scbond_other2.0425.5181296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4688.0571797
X-RAY DIFFRACTIONr_long_range_B_refined6.137602639
X-RAY DIFFRACTIONr_long_range_B_other6.13660.0162640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 48 -
Rwork0.307 863 -
obs--99.89 %

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