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- PDB-7s7u: Crystal structure of iNicSnFR3a Fluorescent Nicotine Sensor with ... -

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Basic information

Entry
Database: PDB / ID: 7s7u
TitleCrystal structure of iNicSnFR3a Fluorescent Nicotine Sensor with nicotine bound
ComponentsiNicSnFR 3.0 Fluorescent Nicotine Sensor
KeywordsFLUORESCENT PROTEIN / nicotine / gfp / periplasmic binding protein / nicotine-binding protein / fluorescent sensor / pharmacokinetic sensor / CHOLINE-BINDING PROTEIN
Function / homologyOsmoprotection protein (prox); domain 2 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsFan, C. / Shivange, A.V. / Looger, L.L. / Lester, H.A. / Rees, D.C.
Funding support United States, 6items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA037161 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA043829 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)GM123582 United States
Tobacco-Related Disease Research Program (TRDRP)23XT-0007 United States
Tobacco-Related Disease Research Program (TRDRP)27IP-0057 United States
Citation
Journal: Elife / Year: 2022
Title: Correction: Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands.
Authors: Nichols, A.L. / Blumenfeld, Z. / Fan, C. / Luebbert, L. / Blom, A.E.M. / Cohen, B.N. / Marvin, J.S. / Borden, P.M. / Kim, C.H. / Muthusamy, A.K. / Shivange, A.V. / Knox, H.J. / Campello, H.R. ...Authors: Nichols, A.L. / Blumenfeld, Z. / Fan, C. / Luebbert, L. / Blom, A.E.M. / Cohen, B.N. / Marvin, J.S. / Borden, P.M. / Kim, C.H. / Muthusamy, A.K. / Shivange, A.V. / Knox, H.J. / Campello, H.R. / Wang, J.H. / Dougherty, D.A. / Looger, L.L. / Gallagher, T. / Rees, D.C. / Lester, H.A.
#1: Journal: Elife / Year: 2022
Title: Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands.
Authors: Nichols, A.L. / Blumenfeld, Z. / Fan, C. / Luebbert, L. / Blom, A.E.M. / Cohen, B.N. / Marvin, J.S. / Borden, P.M. / Kim, C.H. / Muthusamy, A.K. / Shivange, A.V. / Knox, H.J. / Campello, H.R. ...Authors: Nichols, A.L. / Blumenfeld, Z. / Fan, C. / Luebbert, L. / Blom, A.E.M. / Cohen, B.N. / Marvin, J.S. / Borden, P.M. / Kim, C.H. / Muthusamy, A.K. / Shivange, A.V. / Knox, H.J. / Campello, H.R. / Wang, J.H. / Dougherty, D.A. / Looger, L.L. / Gallagher, T. / Rees, D.C. / Lester, H.A.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Structure summary / Category: struct / struct_keywords
Item: _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Apr 27, 2022Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 8, 2023Group: Database references / Category: citation / citation_author
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iNicSnFR 3.0 Fluorescent Nicotine Sensor


Theoretical massNumber of molelcules
Total (without water)60,3291
Polymers60,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.282, 192.282, 49.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein iNicSnFR 3.0 Fluorescent Nicotine Sensor


Mass: 60329.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. X513 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Has ligand of interestY
Has protein modificationY

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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: 4.31 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3,350 0.2 M Sodium malonate, pH 8.0 0.1 M Bistrispropane, pH 8.5
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→39.04 Å / Num. obs: 22632 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 100 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.04 / Rrim(I) all: 0.179 / Χ2: 0.94 / Net I/σ(I): 14.9
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 20.6 % / Rmerge(I) obs: 3.688 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3603 / CC1/2: 0.429 / Rpim(I) all: 0.83 / Rrim(I) all: 3.782 / Χ2: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EFR

6efr


Resolution: 2.95→38.99 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1120 4.98 %
Rwork0.1837 21370 -
obs0.1859 22490 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.61 Å2 / Biso mean: 94.8385 Å2 / Biso min: 35.84 Å2
Refinement stepCycle: final / Resolution: 2.95→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 0 0 4068
Num. residues----512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.080.37661320.32972516264895
3.08-3.240.34531350.30226512786100
3.24-3.450.33211440.251226472791100
3.45-3.710.2721360.209726602796100
3.71-4.080.26081400.217627112851100
4.08-4.670.19661440.143326852829100
4.68-5.890.19741420.167527002842100
5.89-38.990.19021470.151728002947100

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