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

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Basic information

Entry
Database: PDB / ID: 4xto
TitleCrystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 5.6
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 / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.5Jan 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,33520
Polymers164,3955
Non-polymers2,94015
Water27015
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18950 Å2
ΔGint-125 kcal/mol
Surface area42180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.100, 238.980, 132.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Sodium pumping rhodopsin


Mass: 32879.008 Da / Num. of mol.: 5
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.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H42
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
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: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.8→47.3 Å / Num. obs: 47136 / % possible obs: 99.3 % / Redundancy: 4.2 % / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.18 / % possible all: 98.6

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Processing

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

4xtn


Resolution: 2.8→47.3 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 25.683 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R: 1.017 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28016 2482 5 %RANDOM
Rwork0.23002 ---
obs0.23257 47136 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.276 Å2
Baniso -1Baniso -2Baniso -3
1-9.25 Å20 Å2-0 Å2
2---8.69 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10544 0 113 15 10672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0210927
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210478
X-RAY DIFFRACTIONr_angle_refined_deg0.6031.95514825
X-RAY DIFFRACTIONr_angle_other_deg1.0593.00323628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.53851315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0423.795440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.396151640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8311520
X-RAY DIFFRACTIONr_chiral_restr0.0340.21671
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022716
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_it6.4498.0185293
X-RAY DIFFRACTIONr_mcbond_other6.4428.0185292
X-RAY DIFFRACTIONr_mcangle_it9.55812.0236597
X-RAY DIFFRACTIONr_mcangle_other9.55912.0246598
X-RAY DIFFRACTIONr_scbond_it6.448.4515634
X-RAY DIFFRACTIONr_scbond_other6.448.4515635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.88712.498229
X-RAY DIFFRACTIONr_long_range_B_refined12.64567.74713969
X-RAY DIFFRACTIONr_long_range_B_other12.64567.74913970
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 188 -
Rwork0.404 3484 -
obs--99.22 %

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