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- PDB-6edq: Crystal Structure of the Light-Gated Anion Channelrhodopsin GtACR1 -

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Basic information

Entry
Database: PDB / ID: 6edq
TitleCrystal Structure of the Light-Gated Anion Channelrhodopsin GtACR1
ComponentsAnion channelrhodopsin 1
KeywordsMEMBRANE PROTEIN / Cl- channel / membrane proteins
Function / homologyArchaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / identical protein binding / membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Opsin
Function and homology information
Biological speciesGuillardia theta CCMP2712 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, H. / Huang, C.Y. / Wang, M. / Zheng, L. / Spudich, J.L.
Funding support United States, European Union, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM027750 United States
Robert A. Welch FoundationAU-0009 United States
European Union (EU)701647European Union
CitationJournal: Elife / Year: 2019
Title: Crystal structure of a natural light-gated anion channelrhodopsin.
Authors: Li, H. / Huang, C.Y. / Govorunova, E.G. / Schafer, C.T. / Sineshchekov, O.A. / Wang, M. / Zheng, L. / Spudich, J.L.
History
DepositionAug 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anion channelrhodopsin 1
B: Anion channelrhodopsin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,65215
Polymers69,3392
Non-polymers3,31313
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-39 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.790, 149.550, 62.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Anion channelrhodopsin 1


Mass: 34669.555 Da / Num. of mol.: 2 / Fragment: residues 1-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Guillardia theta CCMP2712 (eukaryote) / Gene: GUITHDRAFT_111593 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: L1J207
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6 / Details: 15% MPD, 100 mM ADA, pH 6.0, and 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→47.91 Å / Num. obs: 16711 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 0.994 / Net I/σ(I): 4.54
Reflection shellResolution: 2.9→2.98 Å / Num. unique obs: 7958 / CC1/2: 0.317

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EID

6eid


Resolution: 2.9→47.91 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.83
RfactorNum. reflection% reflection
Rfree0.2668 836 5 %
Rwork0.2297 --
obs0.2317 16711 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 219 22 4568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054658
X-RAY DIFFRACTIONf_angle_d0.8926286
X-RAY DIFFRACTIONf_dihedral_angle_d16.7522722
X-RAY DIFFRACTIONf_chiral_restr0.048702
X-RAY DIFFRACTIONf_plane_restr0.007738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.08170.39221370.35592595X-RAY DIFFRACTION100
3.0817-3.31960.33021370.31632608X-RAY DIFFRACTION100
3.3196-3.65360.29011370.27082598X-RAY DIFFRACTION100
3.6536-4.1820.26021400.20942647X-RAY DIFFRACTION100
4.182-5.26780.23441390.18862659X-RAY DIFFRACTION100
5.2678-47.92050.23161460.19892768X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 44.1841 Å / Origin y: 33.6604 Å / Origin z: 15.651 Å
111213212223313233
T0.5161 Å20.0137 Å2-0.0046 Å2-0.5154 Å2-0.2342 Å2--0.4418 Å2
L1.1023 °20.3738 °2-0.1848 °2-0.5432 °2-0.5097 °2--0.4928 °2
S-0.1091 Å °0.024 Å °0.0134 Å °-0.0605 Å °0.0576 Å °-0.014 Å °0.0639 Å °0.0214 Å °0.0627 Å °
Refinement TLS groupSelection details: all

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