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- PDB-8wew: Haloquadratum walsbyi middle rhodopsin -

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Basic information

Entry
Database: PDB / ID: 8wew
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.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Haloquadratum walsbyi middle rhodopsin at 2.5 Angstroms resolution.
Authors: Ko, L.N. / Lim, G.Z. / Ko, T. / Yang, C.S.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)55,6507
Polymers55,0082
Non-polymers6425
Water70339
1
A: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7892
Polymers27,5041
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-2 kcal/mol
Surface area11310 Å2
MethodPISA
2
B: Bacteriorhodopsin-II-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8625
Polymers27,5041
Non-polymers3574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-12 kcal/mol
Surface area11070 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.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 200mM Lithium sulfate, 100mM imidazole, 30% PEG 400

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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: 13299 / % possible obs: 78.8 % / Redundancy: 14.1 % / CC1/2: 0.97 / Net I/σ(I): 5.64
Reflection shellResolution: 2.5→2.69 Å / Num. unique obs: 2272 / CC1/2: 0.241

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XSCALEdata scaling
XDSdata reduction
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.81 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.863 / SU B: 15.711 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33446 665 5 %RANDOM
Rwork0.28742 ---
obs0.28968 12634 78.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.224 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å2-0 Å2
2---1.69 Å20 Å2
3---3.52 Å2
Refinement stepCycle: 1 / Resolution: 2.5→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 43 39 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0113634
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163637
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.6314962
X-RAY DIFFRACTIONr_angle_other_deg0.4591.5548292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.157522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.23110594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.863.6311862
X-RAY DIFFRACTIONr_mcbond_other3.8593.6311862
X-RAY DIFFRACTIONr_mcangle_it6.7566.5172324
X-RAY DIFFRACTIONr_mcangle_other6.7556.5182325
X-RAY DIFFRACTIONr_scbond_it2.9163.8281772
X-RAY DIFFRACTIONr_scbond_other2.9153.8291773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3136.9492639
X-RAY DIFFRACTIONr_long_range_B_refined10.2334.714520
X-RAY DIFFRACTIONr_long_range_B_other10.22934.724521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 46 -
Rwork0.326 808 -
obs--71.29 %

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