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

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Basic information

Entry
Database: PDB / ID: 7zow
TitleCrystal structure of Synechocystis halorhodopsin (SyHR), Cl-pumping mode, O 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: 1.6 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)31,77119
Polymers26,4631
Non-polymers5,30718
Water2,180121
1
A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules

A: Synechocystis halorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,31257
Polymers79,3893
Non-polymers15,92254
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
Unit cell
Length a, b, c (Å)62.406, 62.406, 110.076
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-1214-

HOH

21A-1220-

HOH

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Components

#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)
#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.49 %
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: 1.6→48.52 Å / Num. obs: 33454 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 17.94 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.227 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
7.16-48.529.521.74430.9990.06998
5.06-7.161120.97400.9990.07699.9
3.58-4.1310.822.99260.9980.07499.9
3.58-4.1310.820.110920.9960.093100
3.2-3.581116.512200.9950.123100
2.92-3.211.214.813240.9950.13799.9
2.7-2.9211.312.914480.9930.163100
2.53-2.710.910.515420.9890.2100
2.39-2.5310.98.516370.9840.261100
2.26-2.3911.17.217360.9730.329100
2.16-2.2611.1617920.9620.406100
2.07-2.1611519170.9390.49199.9
1.98-2.0711.23.919640.9060.655100
1.91-1.9811.22.720340.8260.952100
1.85-1.9111.32.121310.7181.202100
1.79-1.8511.31.721530.6051.476100
1.74-1.7911.21.322500.491.874100
1.69-1.74111.122910.422.139100
1.64-1.6911123740.3492.443100
1.6-1.64110.824400.2892.988100

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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: 1.6→19.28 Å / SU ML: 0.2237 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 1609 5.13 %
Rwork0.195 29754 -
obs0.1969 31363 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.71 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 233 121 2144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622186
X-RAY DIFFRACTIONf_angle_d0.86872911
X-RAY DIFFRACTIONf_chiral_restr0.0533314
X-RAY DIFFRACTIONf_plane_restr0.0058337
X-RAY DIFFRACTIONf_dihedral_angle_d14.5405854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.3667940.28951796X-RAY DIFFRACTION64
1.65-1.710.30331140.29922363X-RAY DIFFRACTION82.27
1.71-1.780.27461300.27032554X-RAY DIFFRACTION89.74
1.78-1.860.32931430.24912720X-RAY DIFFRACTION95.21
1.86-1.960.29431530.23142841X-RAY DIFFRACTION99.8
1.96-2.080.24341540.19842876X-RAY DIFFRACTION100
2.08-2.240.18781220.17292883X-RAY DIFFRACTION99.93
2.24-2.470.22091510.17242884X-RAY DIFFRACTION100
2.47-2.820.21851970.17362873X-RAY DIFFRACTION100
2.82-3.550.21611660.17762909X-RAY DIFFRACTION99.97
3.55-19.280.21141850.1873055X-RAY DIFFRACTION99.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.916332044383-0.3394049281420.03952871298420.712735977174-0.191272532130.7497869996330.0187785286278-0.07602715561760.0634271810240.08818422842860.00643680467238-0.0386204561969-0.0257072594680.0123424022855-0.02190891644590.132620964634-0.01545717462550.004575694926960.127672878064-0.006623853212440.178981865566.7633258525-16.486815623-28.3450796601
20.3907881000880.05412683011330.05962374238490.391118291674-0.08900989629671.092616185510.0141798863892-0.06974011761430.009430319036920.07451089652640.01091290326840.0458409280266-0.0137561377365-0.0670072690626-0.01739395313190.1435887425-0.004907247703420.004477126705770.1309749918-0.005561697725530.139758001368-11.3784056-21.3778542689-29.8501435355
30.528936136554-0.0465866154497-0.07328192401120.711999463841-0.4929066149931.23068468578-0.02757771963890.0001991039648230.0644082378684-0.0221330834813-0.017678301031-0.0297635123153-0.07294644596640.09486225526890.03428632332090.1305798404480.000348558330031-0.002720831592570.113089785191-0.01238418082330.178687463542-3.04368414195-12.1920509579-27.8462963226
41.82152454987-0.5968407737872.265137882920.200262591834-0.7441777572982.82182343018-0.00619797987531-0.258145518752-0.1441603007810.02612471574070.1034927184250.1126256482380.219332029164-0.251838419364-0.1073996388690.693529078809-0.2949464995180.043948027540.897597175994-0.08279132675210.333646553331-1.11742573181-12.6684612863-2.04334633438
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 59 )1 - 591 - 59
22chain 'A' and (resid 60 through 189 )60 - 18960 - 189
33chain 'A' and (resid 190 through 219 )190 - 219190 - 219
44chain 'A' and (resid 220 through 225 )220 - 225220 - 225

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