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- PDB-4xtn: Crystal structure of the light-driven sodium pump KR2 in the pent... -

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Basic information

Entry
Database: PDB / ID: 4xtn
TitleCrystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / ion pump
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 / Chem-MPG / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGushchin, I. / Shevchenko, V. / Polovinkin, V. / Gordeliy, V.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structure of a light-driven sodium pump.
Authors: Gushchin, I. / Shevchenko, V. / Polovinkin, V. / Kovalev, K. / Alekseev, A. / Round, E. / Borshchevskiy, V. / Balandin, T. / Popov, A. / Gensch, T. / Fahlke, C. / Bamann, C. / Willbold, D. / ...Authors: Gushchin, I. / Shevchenko, V. / Polovinkin, V. / Kovalev, K. / Alekseev, A. / Round, E. / Borshchevskiy, V. / Balandin, T. / Popov, A. / Gensch, T. / Fahlke, C. / Bamann, C. / Willbold, D. / Buldt, G. / Bamberg, E. / Gordeliy, V.
History
DepositionJan 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Apr 29, 2015Group: Database references
Revision 1.4May 13, 2015Group: Database references
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Category: pdbx_data_processing_status / struct_conn
Revision 1.6Jan 10, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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.ptnr2_label_seq_id / _struct_conn_type.id

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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
F: Sodium pumping rhodopsin
G: Sodium pumping rhodopsin
H: Sodium pumping rhodopsin
I: Sodium pumping rhodopsin
J: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,926148
Polymers328,79010
Non-polymers37,136138
Water6,323351
1
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)182,96374
Polymers164,3955
Non-polymers18,56869
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Sodium pumping rhodopsin
G: Sodium pumping rhodopsin
H: Sodium pumping rhodopsin
I: Sodium pumping rhodopsin
J: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,96374
Polymers164,3955
Non-polymers18,56869
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.690, 107.000, 240.800
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sodium pumping rhodopsin


Mass: 32879.008 Da / Num. of mol.: 10
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 118 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: The crystals were grown using in meso crystallization technique

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.2→48.9 Å / Num. obs: 192342 / % possible obs: 96.2 % / Redundancy: 2.8 % / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 1.2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTL

4xtl


Resolution: 2.2→48.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.692 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 9797 4.8 %RANDOM
Rwork0.19482 ---
obs0.1968 192342 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.945 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å2-0.19 Å2
2--1.74 Å2-0 Å2
3----3.13 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21636 0 1324 351 23311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0223452
X-RAY DIFFRACTIONr_bond_other_d0.0030.0223749
X-RAY DIFFRACTIONr_angle_refined_deg0.8321.98731348
X-RAY DIFFRACTIONr_angle_other_deg1.1213.00353823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.23152706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78123.949909
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.982153449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.071540
X-RAY DIFFRACTIONr_chiral_restr0.0490.23441
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0225008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025550
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_it3.3293.39510849
X-RAY DIFFRACTIONr_mcbond_other3.3283.39510848
X-RAY DIFFRACTIONr_mcangle_it4.425.07313515
X-RAY DIFFRACTIONr_mcangle_other4.425.07413516
X-RAY DIFFRACTIONr_scbond_it4.1443.83612603
X-RAY DIFFRACTIONr_scbond_other4.1443.83612604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8375.54417824
X-RAY DIFFRACTIONr_long_range_B_refined7.01528.59628382
X-RAY DIFFRACTIONr_long_range_B_other7.01528.59728383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 709 -
Rwork0.314 14410 -
obs--97.84 %

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