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- PDB-6eig: Crystal structure of N24Q/C128T mutant of Channelrhodopsin 2 -

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Basic information

Entry
Database: PDB / ID: 6eig
TitleCrystal structure of N24Q/C128T mutant of Channelrhodopsin 2
ComponentsArchaeal-type opsin 2
KeywordsMEMBRANE PROTEIN / Retinal protein / Ion transport
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / endoplasmic reticulum / plasma membrane / EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Archaeal-type opsin 2
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKovalev, K. / Borshchevskiy, V. / Volkov, O. / Polovinkin, V. / Marin, E. / Balandin, T. / Astashkin, R. / Bamann, C. / Bueldt, G. / Willlbold, D. ...Kovalev, K. / Borshchevskiy, V. / Volkov, O. / Polovinkin, V. / Marin, E. / Balandin, T. / Astashkin, R. / Bamann, C. / Bueldt, G. / Willlbold, D. / Popov, A. / Bamberg, E. / Gordeliy, V.
Funding support France, Germany, Russian Federation, 7items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029-02 France
German Research FoundationCEA(IBS)-HGF(FZJ) STC 5.1 Germany
German Research FoundationSFB 807 Germany
ERA.Net RUS PlusID 323 Russian Federation
Russian Science Foundation16-15-00242 Russian Federation
FRISBIANR-10-INSB-05-02 France
GRALANR-10-LABX-49-01 France
CitationJournal: Science / Year: 2017
Title: Structural insights into ion conduction by channelrhodopsin 2.
Authors: Volkov, O. / Kovalev, K. / Polovinkin, V. / Borshchevskiy, V. / Bamann, C. / Astashkin, R. / Marin, E. / Popov, A. / Balandin, T. / Willbold, D. / Buldt, G. / Bamberg, E. / Gordeliy, V.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaeal-type opsin 2
B: Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,67313
Polymers70,4222
Non-polymers3,25111
Water59433
1
A: Archaeal-type opsin 2
hetero molecules

A: Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,59416
Polymers70,4222
Non-polymers4,17214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6350 Å2
ΔGint-48 kcal/mol
Surface area21020 Å2
MethodPISA
2
B: Archaeal-type opsin 2
hetero molecules

B: Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,75110
Polymers70,4222
Non-polymers2,3298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4460 Å2
ΔGint-58 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.510, 134.060, 78.470
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Archaeal-type opsin 2 / Chlamyopsin 4 light-gated ion channel / Retinal binding protein / Sensory opsin B


Mass: 35210.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: cop4, acop2, COP4, CSOB, CHLREDRAFT_182032 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q8RUT8
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: Sodium-potassium phosphates

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17600 / % possible obs: 96.01 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.142 / Net I/σ(I): 3.5
Reflection shellResolution: 2.7→2.97 Å / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.223 / Rpim(I) all: 0.724

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EID

6eid


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.893 / SU B: 34.544 / SU ML: 0.603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.862 / ESU R Free: 0.411
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2975 860 4.9 %RANDOM
Rwork0.2645 ---
obs0.2662 16688 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 270.26 Å2 / Biso mean: 62.915 Å2 / Biso min: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1-5.61 Å20 Å2-0.51 Å2
2---5.36 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 133 33 4104
Biso mean--102.28 44.07 -
Num. residues----500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0194179
X-RAY DIFFRACTIONr_bond_other_d0.0020.023886
X-RAY DIFFRACTIONr_angle_refined_deg0.4321.9625651
X-RAY DIFFRACTIONr_angle_other_deg0.40638927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7285496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.41222.628156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86115594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4491512
X-RAY DIFFRACTIONr_chiral_restr0.030.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.024520
X-RAY DIFFRACTIONr_gen_planes_other00.02950
LS refinement shellResolution: 2.7→2.769 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 55 -
Rwork0.43 1231 -
all-1286 -
obs--96.62 %

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