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- PDB-6rf6: Crystal structure of the light-driven sodium pump KR2 in the mono... -

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Basic information

Entry
Database: PDB / ID: 6rf6
TitleCrystal structure of the light-driven sodium pump KR2 in the monomeric form, pH 8.0
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: 1.8 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)38,57023
Polymers32,6121
Non-polymers5,95822
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-12 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.411, 82.319, 233.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

21A-479-

HOH

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Components

#1: Protein Sodium pumping rhodopsin


Mass: 32611.580 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
#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-RET / RETINAL


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.16 Å3/Da / Density % sol: 61.13 %
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: ID30B / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→40.6 Å / Num. obs: 36723 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.019 / Rrim(I) all: 0.044 / Net I/σ(I): 19.1 / Num. measured all: 190887
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
1.8-1.845.40.4281172121790.9250.2010.4743.399.9
9-40.64.40.02715383470.9990.0140.03143.397.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTL

4xtl


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.289 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 1416 3.9 %RANDOM
Rwork0.1425 ---
obs0.144 35277 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.22 Å2 / Biso mean: 37.42 Å2 / Biso min: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å2-0 Å20 Å2
2--0.9 Å20 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 186 93 2415
Biso mean--69.43 52.71 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0142516
X-RAY DIFFRACTIONr_bond_other_d00.0182510
X-RAY DIFFRACTIONr_angle_refined_deg0.7671.6973376
X-RAY DIFFRACTIONr_angle_other_deg0.9021.8425821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14823.23299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54315370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.847154
X-RAY DIFFRACTIONr_chiral_restr0.0530.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_rigid_bond_restr6.20835012
X-RAY DIFFRACTIONr_sphericity_free39.61546
X-RAY DIFFRACTIONr_sphericity_bonded21.21954996
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 102 -
Rwork0.196 2547 -
all-2649 -
obs--99.85 %

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