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- PDB-6rfb: Crystal structure of the potassium-pumping S254A mutant of the li... -

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Basic information

Entry
Database: PDB / ID: 6rfb
TitleCrystal structure of the potassium-pumping S254A mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.3
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / light-driven sodium pump / ion translocation / retinal / rhodopsin
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
EICOSANE / RETINAL / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKovalev, K. / Polovinkin, V. / Gushchin, I. / Borshchevskiy, V. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029-02 France
Russian Foundation for Basic Research6.3157.2017/PP Russian Federation
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05-02 France
Grenoble Alliance for Integrated Structural Cell BiologyANR-10-LABX-49-01 France
Russian Science FoundationRSF 16-15-00242 Russian Federation
CitationJournal: Sci Adv / Year: 2019
Title: Structure and mechanisms of sodium-pumping KR2 rhodopsin.
Authors: Kovalev, K. / Polovinkin, V. / Gushchin, I. / Alekseev, A. / Shevchenko, V. / Borshchevskiy, V. / Astashkin, R. / Balandin, T. / Bratanov, D. / Vaganova, S. / Popov, A. / Chupin, V. / Buldt, ...Authors: Kovalev, K. / Polovinkin, V. / Gushchin, I. / Alekseev, A. / Shevchenko, V. / Borshchevskiy, V. / Astashkin, R. / Balandin, T. / Bratanov, D. / Vaganova, S. / Popov, A. / Chupin, V. / Buldt, G. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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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)42,69439
Polymers32,5961
Non-polymers10,09838
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint169 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.796, 83.000, 234.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium pumping rhodopsin


Mass: 32595.580 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

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.78 %
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: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.1→40.78 Å / Num. obs: 23679 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Net I/σ(I): 10.9 / Num. measured all: 107962
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.164.81.674922419360.530.8661.8911100
8.91-40.783.80.017140436710.0090.01946.598.1

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTL

4xtl


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.381 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.198
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 1095 4.6 %RANDOM
Rwork0.2257 ---
obs0.2281 22551 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 159.87 Å2 / Biso mean: 50.253 Å2 / Biso min: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0 Å2
2--6.18 Å20 Å2
3----5.71 Å2
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 292 29 2467
Biso mean--84.34 49.22 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0152458
X-RAY DIFFRACTIONr_bond_other_d00.0182569
X-RAY DIFFRACTIONr_angle_refined_deg0.571.7323217
X-RAY DIFFRACTIONr_angle_other_deg0.7061.9395919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7685267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96623.15292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21315334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.547154
X-RAY DIFFRACTIONr_chiral_restr0.0280.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 78 -
Rwork0.405 1658 -
all-1736 -
obs--99.94 %

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