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- PDB-7zoy: Crystal structure of Synechocystis halorhodopsin (SyHR), SO4-boun... -

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Basic information

Entry
Database: PDB / ID: 7zoy
TitleCrystal structure of Synechocystis halorhodopsin (SyHR), SO4-bound form, ground state
ComponentsSynechocystis halorhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / syhr / trapping / cryo / cryotrapping / o-state / k-state / sulfate / chloride / pump / anion / photocycle / ion transport
Function / homologyEICOSANE / OLEIC ACID
Function and homology information
Biological speciesSynechocystis sp. PCC 7509 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsKovalev, K. / Bukhdruker, S. / Astashkin, R. / Vaganova, S. / Gordeliy, V.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
Ministry of Science and Higher Education of the Russian Federation075-00337-20-03/FSMG-2020-0003 Russian Federation
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-10-LABX-49-01 France
Russian Science Foundation16-15-00242 Russian Federation
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into light-driven anion pumping in cyanobacteria.
Authors: Astashkin, R. / Kovalev, K. / Bukhdruker, S. / Vaganova, S. / Kuzmin, A. / Alekseev, A. / Balandin, T. / Zabelskii, D. / Gushchin, I. / Royant, A. / Volkov, D. / Bourenkov, G. / Koonin, E. / ...Authors: Astashkin, R. / Kovalev, K. / Bukhdruker, S. / Vaganova, S. / Kuzmin, A. / Alekseev, A. / Balandin, T. / Zabelskii, D. / Gushchin, I. / Royant, A. / Volkov, D. / Bourenkov, G. / Koonin, E. / Engelhard, M. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 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

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Assembly

Deposited unit
A: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,92519
Polymers26,4631
Non-polymers4,46218
Water1,33374
1
A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,77457
Polymers79,3893
Non-polymers13,38554
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Unit cell
Length a, b, c (Å)62.300, 62.300, 110.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Synechocystis halorhodopsin


Mass: 26463.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 7509 (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 92 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C20H42
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 2.0 M Ammonium Sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→48.45 Å / Num. obs: 19823 / % possible obs: 99.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 25.53 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.081 / Net I/σ(I): 7.5
Reflection shellResolution: 1.91→1.94 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 992 / CC1/2: 0.399 / Rpim(I) all: 0.816

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYJ

4hyj


Resolution: 1.91→19.27 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 1045 5.29 %
Rwork0.1946 18713 -
obs0.1964 19758 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 1.91→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 177 74 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092161
X-RAY DIFFRACTIONf_angle_d1.51782886
X-RAY DIFFRACTIONf_chiral_restr0.0816315
X-RAY DIFFRACTIONf_plane_restr0.0061328
X-RAY DIFFRACTIONf_dihedral_angle_d19.4161796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.010.29011410.27652607X-RAY DIFFRACTION98.04
2.01-2.140.29121340.21852618X-RAY DIFFRACTION99.93
2.14-2.30.23721310.20372672X-RAY DIFFRACTION100
2.3-2.530.23411400.18922648X-RAY DIFFRACTION100
2.53-2.90.21761730.17222638X-RAY DIFFRACTION100
2.9-3.650.21681580.17632710X-RAY DIFFRACTION99.97
3.65-19.270.21381680.19542820X-RAY DIFFRACTION99.83

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