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- PDB-9jws: Haloquadratum walsbyi middle rhodopsin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9jws
TitleHaloquadratum walsbyi middle rhodopsin
ComponentsBacteriorhodopsin-II-like protein
KeywordsMEMBRANE PROTEIN / middle rhodopsin / photoreceptor / magnesium-associated protein
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
RETINAL / Bacteriorhodopsin-II-like protein
Similarity search - Component
Biological speciesHaloquadratum walsbyi DSM 16790 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKo, L.N. / Lim, G.Z. / Ko, T. / Yang, C.S. / Li, G.Y. / Chen, J.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Rhodopsin from Haloquadratum walsbyi is a light-driven magnesium transporter.
Authors: Ko, L.N. / Lim, G.Z. / Chen, J.C. / Ko, T. / Li, G.Y. / Yang, C.S.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 21, 2025ID: 8WEW
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin-II-like protein
B: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6748
Polymers55,0082
Non-polymers6666
Water21612
1
A: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8374
Polymers27,5041
Non-polymers3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-16 kcal/mol
Surface area10590 Å2
MethodPISA
2
B: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8374
Polymers27,5041
Non-polymers3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-23 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.460, 62.470, 122.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacteriorhodopsin-II-like protein


Mass: 27504.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi DSM 16790 (archaea)
Gene: bop2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18DH5
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5 / Details: 200mM Lithium sulfate, 100mM imidazole, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→43.81 Å / Num. obs: 14429 / % possible obs: 85.2 % / Redundancy: 14.1 % / CC1/2: 0.97 / Net I/σ(I): 5.64
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 2263 / CC1/2: 0.24

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
PHENIXphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.81 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3244 1346 10.17 %
Rwork0.2957 --
obs0.2987 13229 78.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 44 12 3453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.723
X-RAY DIFFRACTIONf_dihedral_angle_d9.532494
X-RAY DIFFRACTIONf_chiral_restr0.038577
X-RAY DIFFRACTIONf_plane_restr0.01572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.35651180.32911048X-RAY DIFFRACTION71
2.59-2.690.35421220.31281093X-RAY DIFFRACTION74
2.69-2.820.32951310.30221078X-RAY DIFFRACTION73
2.82-2.960.30641280.28831093X-RAY DIFFRACTION73
2.96-3.150.29351270.28871145X-RAY DIFFRACTION76
3.15-3.390.34371470.29481212X-RAY DIFFRACTION81
3.39-3.730.32161410.29961270X-RAY DIFFRACTION84
3.73-4.270.30641430.28131324X-RAY DIFFRACTION86
4.27-5.380.34721440.3111256X-RAY DIFFRACTION81
5.39-43.810.30521450.27771364X-RAY DIFFRACTION83

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