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- PDB-3x3c: Crystal structure of the light-driven sodium pump KR2 in neutral state -

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Basic information

Entry
Database: PDB / ID: 3x3c
TitleCrystal structure of the light-driven sodium pump KR2 in neutral state
ComponentsSodium pumping rhodopsin
KeywordsMEMBRANE PROTEIN / light-driven sodium 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
OLEIC ACID / RETINAL / Sodium pumping rhodopsin
Similarity search - Component
Biological speciesDokdonia eikasta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Ishizuka, T. / Hoque, M.R. / Hososhima, S. / Kunitomo, H. ...Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Ishizuka, T. / Hoque, M.R. / Hososhima, S. / Kunitomo, H. / Ito, J. / Yoshizawa, S. / Yamashita, K. / Takemoto, M. / Nishizawa, T. / Taniguchi, R. / Kogure, K. / Maturana, A.D. / Iino, Y. / Yawo, H. / Ishitani, R. / Kandori, H. / Nureki, O.
CitationJournal: Nature / Year: 2015
Title: Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump
Authors: Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Hososhima, S. / Ishizuka, T. / Hoque, M.R. / Kunitomo, H. / Ito, J. / Yoshizawa, S. / Yamashita, K. / Takemoto, ...Authors: Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Hososhima, S. / Ishizuka, T. / Hoque, M.R. / Kunitomo, H. / Ito, J. / Yoshizawa, S. / Yamashita, K. / Takemoto, M. / Nishizawa, T. / Taniguchi, R. / Kogure, K. / Maturana, A.D. / Iino, Y. / Yawo, H. / Ishitani, R. / Kandori, H. / Nureki, O.
History
DepositionJan 18, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 27, 2015Group: Structure summary
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)34,0275
Polymers32,8951
Non-polymers1,1324
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sodium pumping rhodopsin
hetero molecules

A: Sodium pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,05310
Polymers65,7902
Non-polymers2,2648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_335-x-2,-y-2,z1
Buried area5600 Å2
ΔGint-38 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.552, 83.492, 234.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Sodium pumping rhodopsin


Mass: 32894.859 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-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 42% PEG200, 0.1M Tris-HCl pH 8.0, 0.05M MgCl2, lipidic cubic phase, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 11, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 18480 / Num. obs: 18117 / % possible obs: 98 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.29-2.43198.5
2.43-2.6199.9
2.6-2.811100
2.81-3.071100
3.07-3.431100
3.43-3.96189.1
3.96-4.84194.1
4.84-6.8199.8
6.8-50199

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.899 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 884 4.91 %RANDOM
Rwork0.1949 ---
obs0.1967 17988 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→40.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 52 67 2272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082271
X-RAY DIFFRACTIONf_angle_d1.0233074
X-RAY DIFFRACTIONf_dihedral_angle_d14.244799
X-RAY DIFFRACTIONf_chiral_restr0.039343
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.44410.25471460.21522828100
2.4441-2.63280.21111480.18372855100
2.6328-2.89760.22411490.17412879100
2.8976-3.31680.20241480.17992877100
3.3168-4.17810.22561400.1981270293
4.1781-40.90590.25051530.205296397

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