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- PDB-6gyh: Crystal structure of the light-driven proton pump Coccomyxa subel... -

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Basic information

Entry
Database: PDB / ID: 6gyh
TitleCrystal structure of the light-driven proton pump Coccomyxa subellipsoidea Rhodopsin CsR
ComponentsFamily A G protein-coupled receptor-like protein
KeywordsPROTON TRANSPORT / RETINAL / MICROBIAL-TYPE RHODOPSIN / LIGHT-DRIVEN PROTON PUMP / SEVEN TRANS-MEMBRANE / TRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020
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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Family A G protein-coupled receptor-like protein
Similarity search - Component
Biological speciesCoccomyxa subellipsoidea C-169 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSzczepek, M. / Schmidt, A. / Scheerer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB1078 Germany
German Research FoundationUNICAT Germany
CitationJournal: Sci.Signal. / Year: 2019
Title: Design of a light-gated proton channel based on the crystal structure ofCoccomyxarhodopsin.
Authors: Fudim, R. / Szczepek, M. / Vierock, J. / Vogt, A. / Schmidt, A. / Kleinau, G. / Fischer, P. / Bartl, F. / Scheerer, P. / Hegemann, P.
History
DepositionJun 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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: Family A G protein-coupled receptor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8307
Polymers25,7331
Non-polymers2,0976
Water75742
1
A: Family A G protein-coupled receptor-like protein
hetero molecules

A: Family A G protein-coupled receptor-like protein
hetero molecules

A: Family A G protein-coupled receptor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,49121
Polymers77,1993
Non-polymers6,29218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area8970 Å2
ΔGint-31 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.078, 78.078, 143.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Family A G protein-coupled receptor-like protein


Mass: 25733.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccomyxa subellipsoidea C-169 (plant) / Gene: COCSUDRAFT_42526 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I0YUS5
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1-(9Z-octadecenoyl)-rac-glycerol, 10 % cholesterol, 42 % v/v polyethylene glycol 400; 100 mM MES; pH 6.5, 150 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2→32.91 Å / Num. obs: 22100 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rpim(I) all: 0.066 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.357 / Rpim(I) all: 0.901 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AM6

3am6


Resolution: 2→32.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.792 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22493 1155 5.2 %RANDOM
Rwork0.19231 ---
obs0.19398 20932 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.432 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å2-0 Å2
2--0.59 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 2→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 118 42 1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021889
X-RAY DIFFRACTIONr_bond_other_d0.0090.021863
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.9912566
X-RAY DIFFRACTIONr_angle_other_deg2.2972.9554249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.121.14861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95515240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.223157
X-RAY DIFFRACTIONr_chiral_restr0.1930.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022069
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02473
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.213.105903
X-RAY DIFFRACTIONr_mcbond_other2.1813.101902
X-RAY DIFFRACTIONr_mcangle_it2.7644.6451128
X-RAY DIFFRACTIONr_mcangle_other2.7644.6491129
X-RAY DIFFRACTIONr_scbond_it2.0113.393985
X-RAY DIFFRACTIONr_scbond_other1.9823.393985
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2844.9891436
X-RAY DIFFRACTIONr_long_range_B_refined2.98326.2742216
X-RAY DIFFRACTIONr_long_range_B_other2.96926.2692216
X-RAY DIFFRACTIONr_rigid_bond_restr1.29133746
X-RAY DIFFRACTIONr_sphericity_free42.288516
X-RAY DIFFRACTIONr_sphericity_bonded6.34153720
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 82 -
Rwork0.371 1533 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -14.365 Å / Origin y: -34.4103 Å / Origin z: -0.7783 Å
111213212223313233
T0.1327 Å20.033 Å20.0026 Å2-0.1692 Å2-0.0011 Å2--0.0125 Å2
L0.4647 °20.2627 °2-0.6245 °2-0.6557 °2-0.1821 °2--1.6269 °2
S0.0527 Å °-0.0135 Å °0.0438 Å °-0.0136 Å °-0.0101 Å °0.0895 Å °-0.1889 Å °-0.0322 Å °-0.0427 Å °

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