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- PDB-7cry: Structure of Chloride ion pumping rhodopsin (ClR) with NTQ motif ... -

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Entry
Database: PDB / ID: 7cry
TitleStructure of Chloride ion pumping rhodopsin (ClR) with NTQ motif 100 ps after light activation (6.49 mJ/mm2)
ComponentsChloride pumping rhodopsin
KeywordsMEMBRANE PROTEIN / chloride ion pumping rhodopsin / SFX / XFEL / ClR / NTQ
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / OLEIC ACID / RETINAL / Chloride pumping rhodopsin
Function and homology information
Biological speciesNonlabens marinus S1-08 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYun, J.H. / Liu, H. / Lee, W.T. / Schmidt, M.
Funding support China, Korea, Republic Of, United States, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11575021,U1930402,21773012 China
National Research Foundation (NRF, Korea)2019M3E5D6063903, 2017M3A9F6029753, 2018K2A9A2A06024227,2016R1A6A3A04010213 Korea, Republic Of
National Science Foundation (NSF, United States)1231306,1565180,2030466,DE-AC02-76SF00515 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser.
Authors: Yun, J.H. / Li, X. / Yue, J. / Park, J.H. / Jin, Z. / Li, C. / Hu, H. / Shi, Y. / Pandey, S. / Carbajo, S. / Boutet, S. / Hunter, M.S. / Liang, M. / Sierra, R.G. / Lane, T.J. / Zhou, L. / ...Authors: Yun, J.H. / Li, X. / Yue, J. / Park, J.H. / Jin, Z. / Li, C. / Hu, H. / Shi, Y. / Pandey, S. / Carbajo, S. / Boutet, S. / Hunter, M.S. / Liang, M. / Sierra, R.G. / Lane, T.J. / Zhou, L. / Weierstall, U. / Zatsepin, N.A. / Ohki, M. / Tame, J.R.H. / Park, S.Y. / Spence, J.C.H. / Zhang, W. / Schmidt, M. / Lee, W. / Liu, H.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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:
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Assembly

Deposited unit
A: Chloride pumping rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,73111
Polymers29,3991
Non-polymers2,33310
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.370, 50.090, 69.390
Angle α, β, γ (deg.)90.000, 109.690, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Chloride pumping rhodopsin


Mass: 29398.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens marinus S1-08 (bacteria) / Gene: ClR, NMS_1267 / Production host: Escherichia coli (E. coli) / References: UniProt: W8VZW3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: monoolein mixed in syringes

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Oct 23, 2018 / Frequency: 120
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.81→20.9 Å / Num. obs: 30942 / % possible obs: 100 % / Redundancy: 520.6 % / Biso Wilson estimate: 7.68 Å2 / CC1/2: 0.989 / CC star: 0.9972 / Net I/σ(I): 6.37
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 102.7 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1535 / CC1/2: 0.7489 / CC star: 0.9254 / % possible all: 100
Serial crystallography measurementFocal spot size: 1 µm2 / Pulse duration: 100 fsec. / Pulse photon energy: 9.54 keV
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: lcp injector / Injector diameter: 75 µm
Serial crystallography data reductionCrystal hits: 41253 / Frame hits: 78978 / Frames indexed: 41253

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrystFEL0.8data reduction
CrystFEL0.8data scaling
Coot0.8.9.1model building
PHENIX1.18.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g28

5g28


Resolution: 1.85→20.64 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.9115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3208 1373 5.04 %
Rwork0.2578 25896 -
obs0.261 27269 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 121 106 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02352236
X-RAY DIFFRACTIONf_angle_d2.25123013
X-RAY DIFFRACTIONf_chiral_restr0.1022341
X-RAY DIFFRACTIONf_plane_restr0.0128358
X-RAY DIFFRACTIONf_dihedral_angle_d22.1318361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.43151220.36392369X-RAY DIFFRACTION87.16
1.92-1.990.43121390.36832443X-RAY DIFFRACTION91.04
1.99-2.080.37851260.34372487X-RAY DIFFRACTION92.01
2.08-2.190.36641210.33812553X-RAY DIFFRACTION93.79
2.19-2.330.36521530.32392580X-RAY DIFFRACTION96.1
2.33-2.510.37671430.29492637X-RAY DIFFRACTION96.06
2.51-2.760.3241420.26922648X-RAY DIFFRACTION97.14
2.76-3.160.3061480.23852660X-RAY DIFFRACTION98.01
3.16-3.980.23641450.18232729X-RAY DIFFRACTION98.97
3.98-20.640.22121340.1462790X-RAY DIFFRACTION99.15

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