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- PDB-9ork: Antarctic Rhodopsin crystallized in LCP at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 9ork
TitleAntarctic Rhodopsin crystallized in LCP at pH 8.5
ComponentsAntarctic Rhodopsin
KeywordsMEMBRANE PROTEIN / microbial rhodopsin / retinal-binding protein / inward proton pump
Function / homologyDODECANE / HEXANE / RETINAL
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsPeng, S. / Besaw, J.E. / Ernst, O.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-05764 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06862 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 22, 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)25,9087
Polymers24,8561
Non-polymers1,0526
Water36020
1
AA1: Antarctic Rhodopsin
hetero molecules

AA1: Antarctic Rhodopsin
hetero molecules

AA1: Antarctic Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,72421
Polymers74,5683
Non-polymers3,15618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12010 Å2
ΔGint-31 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.613, 107.613, 50.617
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-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#3: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 279.15 K / Method: lipidic cubic phase / pH: 8.5
Details: 0.2 M NaCl, 20% w/v 2-methyl-2,4-pentanediol, 4% w/v glycerol
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.59→28.91 Å / Num. obs: 10412 / % possible obs: 97.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 52.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.2
Reflection shellResolution: 2.59→2.66 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 738 / CC1/2: 0.762 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→28.91 Å / SU ML: 0.2552 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1032 9.92 %
Rwork0.191 9375 -
obs0.1938 10407 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.63 Å2
Refinement stepCycle: LAST / Resolution: 2.59→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 74 20 1723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861743
X-RAY DIFFRACTIONf_angle_d1.00242346
X-RAY DIFFRACTIONf_chiral_restr0.3211265
X-RAY DIFFRACTIONf_plane_restr0.005277
X-RAY DIFFRACTIONf_dihedral_angle_d14.5865994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.730.28321460.23521293X-RAY DIFFRACTION96
2.73-2.90.29011450.20851313X-RAY DIFFRACTION96.24
2.9-3.130.27381490.20471352X-RAY DIFFRACTION99.08
3.13-3.440.24961460.18521338X-RAY DIFFRACTION98.28
3.44-3.940.21651500.17851352X-RAY DIFFRACTION98.3
3.94-4.960.18531450.17641360X-RAY DIFFRACTION97.85
4.96-28.910.19371510.19911367X-RAY DIFFRACTION94.99

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