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- PDB-9or2: Antarctic Rhodopsin crystallized in bicelles at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 9or2
TitleAntarctic Rhodopsin crystallized in bicelles at pH 4.0
ComponentsAntarctic Rhodopsin
KeywordsMEMBRANE PROTEIN / microbial rhodopsin / retinal-binding protein / inward proton pump
Function / homology1,2-Distearoyl-sn-glycerophosphoethanolamine / DODECANE / RETINAL
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsBesaw, J.E. / Peng, S. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-05764 Canada
CitationJournal: Biophys.J. / Year: 2025
Title: Structural insights into an inward proton pumping rhodopsin.
Authors: Besaw, J.E. / Peng, S. / Kuo, A. / Reichenwallner, J. / Miller, R.J.D. / Brown, L.S. / Ernst, O.P.
History
DepositionMay 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA1: Antarctic Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1487
Polymers24,8561
Non-polymers2,2926
Water91951
1
AA1: Antarctic Rhodopsin
hetero molecules

AA1: Antarctic Rhodopsin
hetero molecules

AA1: Antarctic Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,44321
Polymers74,5683
Non-polymers6,87518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area17460 Å2
ΔGint-85 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.356, 108.356, 54.733
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein Antarctic Rhodopsin


Mass: 24856.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.73 Å3/Da / Density % sol: 67.04 % / Description: Hexagon
Crystal growTemperature: 307.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.2 M - 3.6 M sodium phosphate monobasic monohydrate, pH 4.0, 180 mM 1,6-hexanediol, 3.5% triethylene glycol
PH range: 4.0 - 4.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.07→29.76 Å / Num. obs: 22686 / % possible obs: 99.4 % / Redundancy: 16.5 % / Biso Wilson estimate: 34.73 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.9
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1796 / CC1/2: 0.44 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→29.76 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 1997 8.81 %
Rwork0.2014 20667 -
obs0.2023 22664 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.86 Å2
Refinement stepCycle: LAST / Resolution: 2.07→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 130 51 1832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01681821
X-RAY DIFFRACTIONf_angle_d1.3572444
X-RAY DIFFRACTIONf_chiral_restr0.0808270
X-RAY DIFFRACTIONf_plane_restr0.008283
X-RAY DIFFRACTIONf_dihedral_angle_d19.5418651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.120.33231400.27961487X-RAY DIFFRACTION99.82
2.12-2.180.26181400.25511473X-RAY DIFFRACTION99.81
2.18-2.240.2591410.2171461X-RAY DIFFRACTION100
2.24-2.320.25521390.21591468X-RAY DIFFRACTION99.88
2.32-2.40.22461420.2081475X-RAY DIFFRACTION99.88
2.4-2.490.19711460.20181486X-RAY DIFFRACTION99.76
2.49-2.610.21731400.18941455X-RAY DIFFRACTION99.25
2.61-2.750.19791430.17771477X-RAY DIFFRACTION99.51
2.75-2.920.17731430.17661462X-RAY DIFFRACTION99.5
2.92-3.140.18171450.18251473X-RAY DIFFRACTION99.2
3.14-3.460.21391420.18981473X-RAY DIFFRACTION98.84
3.46-3.960.22181490.20361468X-RAY DIFFRACTION98.36
3.96-4.980.19161420.19621494X-RAY DIFFRACTION97.91
4.98-29.760.2151450.21661515X-RAY DIFFRACTION96.12

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