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- PDB-8xhw: Haloquadratum walsbyi middle rhodopsin mutant - D84N -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8xhw
TitleHaloquadratum walsbyi middle rhodopsin mutant - D84N
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: 2.94 Å
AuthorsKo, L.N. / Lim, G.Z. / Li, G.Y. / Chen, J.C. / Yang, C.S.
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
DepositionDec 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: 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
C: Bacteriorhodopsin-II-like protein
D: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8358
Polymers106,6974
Non-polymers1,1384
Water00
1
A: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9592
Polymers26,6741
Non-polymers2841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9592
Polymers26,6741
Non-polymers2841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9592
Polymers26,6741
Non-polymers2841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9592
Polymers26,6741
Non-polymers2841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.366, 61.367, 118.793
Angle α, β, γ (deg.)90.00, 93.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bacteriorhodopsin-II-like protein / Bacteriorhodopsin-II / Middle rhodopsin / HwMR


Mass: 26674.309 Da / Num. of mol.: 4 / Mutation: D84N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi DSM 16790 (archaea)
Gene: bop2, bopII, HQ_1017A / Production host: Escherichia coli (E. coli) / References: UniProt: Q18DH5
#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 289 K / Method: lipidic cubic phase / pH: 4.5 / Details: 50 mM sodium citrate, 50 mM NaCl, 15% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→30 Å / Num. obs: 17666 / % possible obs: 96.34 % / Redundancy: 1.9 % / Rrim(I) all: 0.231 / Net I/σ(I): 6.3
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 766 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIX(1.19.2_4158)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8WEW

8wew
PDB Unreleased entry


Resolution: 2.94→29.7 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1775 10.05 %Random
Rwork0.2391 ---
obs0.2426 17666 92.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 80 0 6636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.542
X-RAY DIFFRACTIONf_dihedral_angle_d16.4072332
X-RAY DIFFRACTIONf_chiral_restr0.0361112
X-RAY DIFFRACTIONf_plane_restr0.0041096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.020.38681110.31021043X-RAY DIFFRACTION80
3.02-3.10.361300.30151086X-RAY DIFFRACTION83
3.1-3.20.32091330.29451128X-RAY DIFFRACTION86
3.2-3.320.29381230.25971137X-RAY DIFFRACTION88
3.32-3.450.3291350.26741151X-RAY DIFFRACTION88
3.45-3.610.26641320.24731216X-RAY DIFFRACTION89
3.61-3.80.30361330.23371189X-RAY DIFFRACTION93
3.8-4.040.21441430.21441273X-RAY DIFFRACTION98
4.04-4.350.21561410.19091334X-RAY DIFFRACTION100
4.35-4.780.24771440.19651326X-RAY DIFFRACTION100
4.78-5.470.28051460.23311324X-RAY DIFFRACTION100
5.47-6.880.33851450.26361352X-RAY DIFFRACTION100
6.88-29.70.23011590.23011332X-RAY DIFFRACTION98

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