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

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Basic information

Entry
Database: PDB / ID: 7znb
TitleCrystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the M state at pH 5.2 in the presence of sodium at 100K
Componentsxenorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle
Function / homologyEICOSANE / OLEIC ACID / PHOSPHATE ION
Function and homology information
Biological speciesBacillus coahuilensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)94,31865
Polymers77,1773
Non-polymers17,14162
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29290 Å2
ΔGint171 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.500, 109.500, 119.000
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 / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 223 / Label seq-ID: 1 - 223

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 282.547 Da / Num. of mol.: 44 / 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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.8 M Na/K-Pi pH 8.2 crystals soaked in 1.2 M Na/K-Pi pH 5.2 before harvesting

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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: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→49.738 Å / Num. obs: 62940 / % possible obs: 95.3 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→1.963 Å / Rmerge(I) obs: 1.948 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3149 / CC1/2: 0.554

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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: 1.9→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.345 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 3046 4.8 %RANDOM
Rwork0.1966 ---
obs0.1981 59830 88.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.72 Å2 / Biso mean: 33.732 Å2 / Biso min: 16.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--0.19 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5245 0 637 240 6122
Biso mean--58.35 44.43 -
Num. residues----666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156653
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.6438165
X-RAY DIFFRACTIONr_angle_other_deg1.0451.54515275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5995697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.65518.873213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90615856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9841519
X-RAY DIFFRACTIONr_chiral_restr0.0490.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026290
X-RAY DIFFRACTIONr_gen_planes_other00.021324
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A7717
12B7717
21A7780
22C7780
31B7718
32C7718
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 104 -
Rwork0.302 2257 -
all-2361 -
obs--45.58 %

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