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- PDB-5b0w: Crystal structure of the 11-cis isomer of pharaonis halorhodopsin... -

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Basic information

Entry
Database: PDB / ID: 5b0w
TitleCrystal structure of the 11-cis isomer of pharaonis halorhodopsin in the absence of halide ions
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / seven trans-membrane helices / retinylidene protein / light-driven chloride ion pump microbial rhodopsin
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / BACTERIORUBERIN / ISOLEUCINE / Chem-L3P / RETINAL / :
Function and homology information
Biological speciesNatronomonas pharaonis DSM 2160 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKouyama, T. / Chan, S.K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States
Authors: Chan, S.K. / Kawaguchi, H. / Kubo, H. / Murakami, M. / Ihara, K. / Maki, K. / Kouyama, T.
History
DepositionNov 11, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
E: Halorhodopsin
F: Halorhodopsin
G: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,88527
Polymers185,8516
Non-polymers10,03521
Water7,999444
1
A: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,40114
Polymers92,9253
Non-polymers5,47611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Halorhodopsin
F: Halorhodopsin
G: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,48413
Polymers92,9253
Non-polymers4,55910
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.320, 97.930, 101.530
Angle α, β, γ (deg.)90.00, 128.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

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Protein / Sugars , 2 types, 13 molecules ABDEFG

#1: Protein
Halorhodopsin


Mass: 30975.096 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Natronomonas pharaonis DSM 2160 (archaea) / Strain: DSM 2160 / References: UniProt: Q3ITX1
#5: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 458 molecules

#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H76O4
#4: Chemical
ChemComp-L3P / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE


Mass: 885.179 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C46H94O11P2
#6: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 1.61 Å3/Da / Density % sol: 23.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6
Details: A mixture solution containing 3mg/ml halorhodopsin, 1M ammonium sulfate, 0.1M NaCl, 0.1 M sodium citrate, and 5.7mg/ml nonylglucoside was concentrated by the sitting-drop vapor diffusion ...Details: A mixture solution containing 3mg/ml halorhodopsin, 1M ammonium sulfate, 0.1M NaCl, 0.1 M sodium citrate, and 5.7mg/ml nonylglucoside was concentrated by the sitting-drop vapor diffusion method. Before data collection, the crystal was soaked in an alkaline solution containing no halide ions, illuminated with red light, and then soaked in a solution at pH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 11, 2015
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50.7 Å / Num. obs: 125077 / % possible obs: 96.8 % / Observed criterion σ(F): 2.5 / Redundancy: 3.2 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.4 / % possible all: 81.8

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Processing

Software
NameVersionClassification
iMOSFLMdata collection
iMOSFLMdata processing
SCALAdata scaling
XTALVIEWmodel building
MOLREPphasing
CNS1.21refinement
SCALAdata reduction
RefinementResolution: 1.7→15 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2154 5461 4.2 %
Rwork0.202 --
obs-124943 96.7 %
Solvent computationBsol: 93.7278 Å2
Displacement parametersBiso max: 112.27 Å2 / Biso mean: 22.3454 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.568 Å20 Å22.017 Å2
2--0.483 Å20 Å2
3----2.051 Å2
Refinement stepCycle: final / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11774 0 432 444 12650
Biso mean--58.72 26.25 -
Num. residues----1559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d1.45

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