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- PDB-7zov: Crystal structure of Synechocystis halorhodopsin (SyHR), Cl-pumpi... -

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Basic information

Entry
Database: PDB / ID: 7zov
TitleCrystal structure of Synechocystis halorhodopsin (SyHR), Cl-pumping mode, K 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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Function and homology information
Biological speciesSynechocystis sp. PCC 7509 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,22322
Polymers26,4631
Non-polymers5,76021
Water2,252125
1
A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,66866
Polymers79,3893
Non-polymers17,27963
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
Buried area21540 Å2
ΔGint-109 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.990, 61.990, 109.820
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-813-

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 , 5 types, 146 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.6 / Details: 1.6 M Ammonium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→48.23 Å / Num. obs: 27378 / % possible obs: 99.2 % / Redundancy: 10.7 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.101 / Net I/σ(I): 5.5
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1379 / CC1/2: 0.306 / Rpim(I) all: 0.975

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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: 1.7→19.95 Å / SU ML: 0.2227 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 1416 5.19 %
Rwork0.1849 25847 -
obs0.1869 27263 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.75 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 239 125 2154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062258
X-RAY DIFFRACTIONf_angle_d0.81633010
X-RAY DIFFRACTIONf_chiral_restr0.0502316
X-RAY DIFFRACTIONf_plane_restr0.0063350
X-RAY DIFFRACTIONf_dihedral_angle_d16.1613885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.32681170.29342369X-RAY DIFFRACTION90.96
1.76-1.830.29921380.26012525X-RAY DIFFRACTION98.63
1.83-1.910.32961380.25372576X-RAY DIFFRACTION100
1.91-2.020.24641300.21152580X-RAY DIFFRACTION100
2.02-2.140.23221320.18652603X-RAY DIFFRACTION99.96
2.14-2.310.17931360.172596X-RAY DIFFRACTION99.93
2.31-2.540.22721370.17832600X-RAY DIFFRACTION99.96
2.54-2.90.21231670.1542619X-RAY DIFFRACTION100
2.9-3.660.19411540.16592649X-RAY DIFFRACTION99.89
3.66-19.950.20321670.17452730X-RAY DIFFRACTION98.87

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