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- PDB-7pnc: Dark state structure of Sensory Rhodopsin II solved by serial mil... -

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Basic information

Entry
Database: PDB / ID: 7pnc
TitleDark state structure of Sensory Rhodopsin II solved by serial millisecond crystallography
ComponentsSensory rhodopsin-2
KeywordsSIGNALING PROTEIN / SRII / serial millisecond crystallography / sensory rhodopsin / sensory rhodopsin II / SMX / SSX
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Chem-MPG / RETINAL / Sensory rhodopsin-2
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBosman, R. / Ortolani, G. / Branden, G. / Neutze, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission637295European Union
CitationJournal: To Be Published
Title: Structural basis of the prolonged photocycle of Sensory Rhodopsin II revealed by serial millisecond crystallography
Authors: Bosman, R. / Ortolani, G. / Branden, G. / Neutze, R.
History
DepositionSep 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensory rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,50018
Polymers26,6661
Non-polymers4,83417
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint11 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.750, 131.700, 51.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

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Protein / Sugars , 2 types, 9 molecules A

#1: Protein Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II


Mass: 26666.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host: Escherichia coli (E. coli) / References: UniProt: P42196
#4: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 47 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase
Details: CaCl 150mM, Glycine 100mM, 38%(v/v) PEG 400, pH 7.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000342 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000342 Å / Relative weight: 1
ReflectionResolution: 2.1→39.44 Å / Num. obs: 18087 / % possible obs: 100 % / Redundancy: 242 % / Biso Wilson estimate: 33.33 Å2 / CC1/2: 0.991 / CC star: 0.998 / R split: 0.1399 / Net I/σ(I): 5.56
Reflection shellResolution: 2.11→2.14 Å / Num. unique obs: 1722 / CC1/2: 0.31 / CC star: 0.686
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H68

1h68


Resolution: 2.2→39.44 Å / SU ML: 0.1991 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2009 781 4.97 %
Rwork0.1832 14948 -
obs0.1841 15729 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 316 38 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411995
X-RAY DIFFRACTIONf_angle_d0.80252672
X-RAY DIFFRACTIONf_chiral_restr0.0391328
X-RAY DIFFRACTIONf_plane_restr0.0038293
X-RAY DIFFRACTIONf_dihedral_angle_d19.7269381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.25791270.24662415X-RAY DIFFRACTION99.88
2.34-2.520.25411190.212476X-RAY DIFFRACTION99.92
2.52-2.770.21251310.18492466X-RAY DIFFRACTION99.88
2.77-3.170.20661290.1742481X-RAY DIFFRACTION100
3.17-40.17651260.1652508X-RAY DIFFRACTION100
4-39.440.18911490.17812602X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: 33.0000789233 Å / Origin y: 37.184319392 Å / Origin z: 2.1600188139 Å
111213212223313233
T0.127677520295 Å20.00683250287654 Å2-0.0154418948179 Å2-0.169374527488 Å20.00254174024477 Å2--0.155043539414 Å2
L0.0634776045001 °2-0.0704400429386 °2-0.560081543289 °2-1.08583257013 °20.0527306044466 °2--1.35087971919 °2
S-0.0162790195721 Å °-0.0693178466995 Å °-0.0266340689227 Å °0.0434320226684 Å °-0.0417699064869 Å °-0.0486218901243 Å °-0.0691941959271 Å °0.131464787175 Å °2.99644956771E-11 Å °
Refinement TLS groupSelection details: all

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