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- PDB-7s7t: iNicSnFR3a Nicotine Sensor comprising Periplasmic Binding sequenc... -

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Basic information

Entry
Database: PDB / ID: 7s7t
TitleiNicSnFR3a Nicotine Sensor comprising Periplasmic Binding sequence plus Fluorescent Sequence with varenicline 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 / homologyIODIDE ION / VARENICLINE
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iNicSnFR 3.0 Fluorescent Nicotine Sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3028
Polymers60,3291
Non-polymers9737
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)190.366, 190.366, 49.742
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)
#2: Chemical ChemComp-QMR / VARENICLINE


Mass: 211.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, agonist*YM
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
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: 4.31 Å3/Da / Density % sol: 71.44 %
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: 1.7711 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7711 Å / Relative weight: 1
ReflectionResolution: 3.2→38.87 Å / Num. obs: 17371 / % possible obs: 99.5 % / Redundancy: 19.3 % / Biso Wilson estimate: 113.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.03183 / Net I/σ(I): 17.7
Reflection shellResolution: 3.203→3.318 Å / Redundancy: 18.7 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 1669 / CC1/2: 0.666 / CC star: 0.894 / Rpim(I) all: 0.6106 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.17.1_3660refinement
PHASERphasing
AutoSolphasing
Aimlessdata scaling
XDSdata processing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EFR

6efr


Resolution: 3.2→38.87 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2188 1723 9.96 %
Rwork0.1867 --
obs0.1901 17300 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.16 Å2 / Biso mean: 118.1649 Å2 / Biso min: 57.92 Å2
Refinement stepCycle: final / Resolution: 3.2→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 16 0 4063
Biso mean--133.04 --
Num. residues----516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.30.36251330.33211245137896
3.3-3.40.4011460.310912801426100
3.4-3.530.30781400.250812901430100
3.53-3.670.311440.235812751419100
3.67-3.830.30631440.232713101454100
3.83-4.030.24321420.208412631405100
4.04-4.290.17631400.15813001440100
4.29-4.620.20081440.145812911435100
4.62-5.080.18691420.144213091451100
5.08-5.820.191440.166513231467100
5.82-7.320.21641500.203613181468100
7.32-38.870.18271540.174513731527100
Refinement TLS params.Method: refined / Origin x: 68.252 Å / Origin y: -81.6203 Å / Origin z: 6.2191 Å
111213212223313233
T0.7594 Å2-0.104 Å2-0.0555 Å2-0.8406 Å2-0.0597 Å2--0.5924 Å2
L2.9483 °20.9035 °2-0.4136 °2-3.3837 °2-0.786 °2--1.8785 °2
S-0.035 Å °-0.2271 Å °-0.3996 Å °-0.309 Å °-0.0198 Å °0.1019 Å °0.378 Å °-0.2042 Å °0.0688 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 601
2X-RAY DIFFRACTION1allZ1 - 6

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