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- PDB-5etz: Structure of the all-trans isomer of pharaonis halorhodopsin in t... -

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Basic information

Entry
Database: PDB / ID: 5etz
TitleStructure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions
ComponentsHalorhodopsin
KeywordsMEMBRANE PROTEIN / retinal protein / light-driven / chloride ion pump / seven-transmembrane / alpha helices
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / BACTERIORUBERIN / Chem-L3P / RETINAL / :
Function and homology information
Biological speciesNatronomonas pharaonis DSM 2160 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKouyama, T.
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 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Feb 19, 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
Revision 1.4Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Halorhodopsin
B: Halorhodopsin
D: Halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,66919
Polymers92,9253
Non-polymers8,74416
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-88 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.400, 97.770, 101.620
Angle α, β, γ (deg.)90.00, 128.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 9 molecules ABD

#1: Protein Halorhodopsin


Mass: 30975.096 Da / Num. of mol.: 3 / 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 / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 6
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 , 4 types, 237 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.22 Å3/Da / Density % sol: 61.75 % / Description: the crystal mosaicity was 0.97.
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The crystal was prepared by the membrane fusion method. A mixture solution containing 3 mg/ml halorhodopsin, 9 mg/ml nonylglucoside, 1 M ammonium sulfate, 0.1 M sodium azide was concentrated ...Details: The crystal was prepared by the membrane fusion method. A mixture solution containing 3 mg/ml halorhodopsin, 9 mg/ml nonylglucoside, 1 M ammonium sulfate, 0.1 M sodium azide was concentrated by the sitting-drop vapor diffusion method. The crystal soaking in a halide-ion-free solution was performed under dim red light, and then the crystal was rapidly cooled with liquid propane at 87 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2015
RadiationMonochromator: Silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50.77 Å / Num. all: 99234 / Num. obs: 99234 / % possible obs: 91.3 % / Observed criterion σ(I): 2.5 / Redundancy: 3.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.7 / % possible all: 60.9

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Processing

Software
NameVersionClassification
CNS1.21refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
XTALVIEWmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qbg

3qbg


Resolution: 1.8→15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 5001 4.6 %Random selection
Rwork0.2185 ---
obs-99008 91.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.919 Å2
2--2.01 Å20 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5900 0 343 227 6470

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