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- PDB-7zmy: Crystal structure of the light-driven inward proton pump xenorhod... -

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Basic information

Entry
Database: PDB / ID: 7zmy
TitleCrystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the ground state at pH 8.2 in the presence of sodium at 100K
Componentsxenorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle
Function / homologyEICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION
Function and homology information
Biological speciesBacillus coahuilensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKovalev, K. / Tsybrov, F. / Alekseev, A. / Bourenkov, G. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Mechanisms of inward transmembrane proton translocation.
Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / ...Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / Chizhov, I. / Royant, A. / Kuzmin, A. / Gushchin, I. / Rosselli, R. / Rodriguez-Valera, F. / Ilyinskiy, N. / Rogachev, A. / Borshchevskiy, V. / Schneider, T.R. / Bamberg, E. / Gordeliy, V.
History
DepositionApr 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Derived calculations / Category: struct_conn
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 26, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Feb 7, 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: xenorhodopsin
B: xenorhodopsin
C: xenorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,43975
Polymers77,1773
Non-polymers19,26272
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32270 Å2
ΔGint165 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.240, 109.570, 119.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: FME / Beg label comp-ID: FME / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA1 - 2231 - 223
21GLNGLNBB1 - 2231 - 223
12SERSERAA1 - 2241 - 224
22SERSERCC1 - 2241 - 224
13HISHISBB1 - 2221 - 222
23HISHISCC1 - 2221 - 222

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein xenorhodopsin


Mass: 25725.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coahuilensis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 352 molecules

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


Mass: 282.547 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 16 / 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.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.8 M Na/K-Pi pH 8.2

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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 EIGER2 X 16M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→49.799 Å / Num. obs: 91083 / % possible obs: 93.12 % / Redundancy: 13.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.742 Å / Rmerge(I) obs: 3.353 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4556 / CC1/2: 0.352 / % possible all: 78.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIO

1xio


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.423 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 4504 4.9 %RANDOM
Rwork0.1745 ---
obs0.176 86518 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.18 Å2 / Biso mean: 33.56 Å2 / Biso min: 18.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.3 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 0 750 283 6295
Biso mean--60.18 45.94 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136195
X-RAY DIFFRACTIONr_bond_other_d00.0156805
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6488188
X-RAY DIFFRACTIONr_angle_other_deg1.2381.54415641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9245690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.25118.657216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29615849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4041520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026244
X-RAY DIFFRACTIONr_gen_planes_other00.021312
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A77760.09
12B77760.09
21A77650.09
22C77650.09
31B77290.08
32C77290.08
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 227 -
Rwork0.334 4526 -
all-4753 -
obs--65.84 %

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