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- PDB-5b2n: Crystal structure of the light-driven chloride ion-pumping rhodop... -

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Basic information

Entry
Database: PDB / ID: 5b2n
TitleCrystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus
ComponentsChloride pumping rhodopsin
KeywordsTRANSPORT PROTEIN / RETINAL / CELL-FREE SYNTHESIS / LIGHT-DRIVEN CHLORIDE PUMP / membrane protein
Function / homology
Function and homology information


photoreceptor activity / phototransduction / membrane
Similarity search - Function
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
DECANE / DODECANE / HEXANE / N-OCTANE / RETINAL / Chloride pumping rhodopsin
Similarity search - Component
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.581 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3
Authors: Hosaka, T. / Yoshizawa, S. / Nakajima, Y. / Ohsawa, N. / Hato, M. / DeLong, E.F. / Kogure, K. / Yokoyama, S. / Kimura-Someya, T. / Iwasaki, W. / Shirouzu, M.
History
DepositionJan 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,59815
Polymers30,7111
Non-polymers1,88714
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint15 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.580, 49.790, 75.320
Angle α, β, γ (deg.)90.000, 130.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chloride pumping rhodopsin


Mass: 30710.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3

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Non-polymers , 7 types, 110 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#5: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#6: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 0.1M Tris-HCl (pH 8.0), 450mM ammonium formate, 40% polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→37.38 Å / Num. obs: 38990 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 19.65 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.089 / Χ2: 1.022 / Net I/σ(I): 11.57 / Num. measured all: 159713
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.58-1.640.7260.8621.6625504636662030.98897.4
1.64-1.790.8530.5622.7624273593258420.64498.5
1.79-1.940.940.3215.0722808556154970.36898.8
1.94-2.120.9760.1818.720962512450630.20898.8
2.12-2.370.9890.10613.6819117469046460.12299.1
2.37-2.730.9940.07218.4816557409840630.08399.1
2.73-3.340.9960.05223.9413823349634570.0698.9
3.34-4.710.9970.03830.510565273326880.04498.4
4.710.9980.03332.376103157715300.03897

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.58 Å37.38 Å
Translation6.24 Å37.38 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIX(1.10.1_2155: 000)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AWZ

5awz


Resolution: 1.581→37.38 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1955 5.02 %Random selection
Rwork0.1758 37007 --
obs0.1769 38962 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.35 Å2 / Biso mean: 23.2188 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 1.581→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 131 96 2291
Biso mean--38.48 37.51 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062251
X-RAY DIFFRACTIONf_angle_d0.8683015
X-RAY DIFFRACTIONf_chiral_restr0.05340
X-RAY DIFFRACTIONf_plane_restr0.005354
X-RAY DIFFRACTIONf_dihedral_angle_d11.2881293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5809-1.62040.35651430.35042598X-RAY DIFFRACTION97
1.6204-1.66420.34941350.2882594X-RAY DIFFRACTION98
1.6642-1.71320.27661400.2542632X-RAY DIFFRACTION98
1.7132-1.76850.2461370.22852586X-RAY DIFFRACTION99
1.7685-1.83170.23441380.19752646X-RAY DIFFRACTION99
1.8317-1.90510.211380.17892599X-RAY DIFFRACTION99
1.9051-1.99180.19861440.17592642X-RAY DIFFRACTION99
1.9918-2.09680.21561380.14782679X-RAY DIFFRACTION99
2.0968-2.22810.17281350.14362635X-RAY DIFFRACTION100
2.2281-2.40010.17541480.14782641X-RAY DIFFRACTION100
2.4001-2.64160.16781370.14462681X-RAY DIFFRACTION100
2.6416-3.02370.14931410.14872675X-RAY DIFFRACTION100
3.0237-3.80890.16921430.16812671X-RAY DIFFRACTION99
3.8089-37.39060.221380.19342728X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5908-0.15772.150.4109-0.13614.65550.04920.08130.0177-0.0794-0.0532-0.0166-0.01280.14960.02260.1589-0.00690.02040.1710.01060.191940.196718.7644-9.0983
20.66430.09090.37220.6454-0.04563.4031-0.0041-0.0462-0.06570.0064-0.0017-0.04320.1805-0.0673-0.00360.1216-0.01590.01980.09930.00390.154232.94214.95592.8199
32.1518-0.33161.03880.5484-0.97641.85210.0774-0.18630.06610.12580.00620.0065-0.20310.04680.00650.1526-0.0250.03810.1273-0.01890.161937.753219.57758.4708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 91 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 264 )A0

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