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- PDB-7s7v: Crystal structure of iNicSnFR3a Fluorescent Nicotine Sensor -

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Basic information

Entry
Database: PDB / ID: 7s7v
TitleCrystal structure of iNicSnFR3a Fluorescent Nicotine Sensor
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: 2.5 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: iNicSnFR 3.0 Fluorescent Nicotine Sensor
B: iNicSnFR 3.0 Fluorescent Nicotine Sensor
C: iNicSnFR 3.0 Fluorescent Nicotine Sensor
D: iNicSnFR 3.0 Fluorescent Nicotine Sensor


Theoretical massNumber of molelcules
Total (without water)241,3174
Polymers241,3174
Non-polymers00
Water9,224512
1
A: iNicSnFR 3.0 Fluorescent Nicotine Sensor


  • defined by author&software
  • 60.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,3291
Polymers60,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: iNicSnFR 3.0 Fluorescent Nicotine Sensor


  • defined by author&software
  • 60.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,3291
Polymers60,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: iNicSnFR 3.0 Fluorescent Nicotine Sensor


  • defined by author&software
  • 60.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,3291
Polymers60,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: iNicSnFR 3.0 Fluorescent Nicotine Sensor


  • defined by author&software
  • 60.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)60,3291
Polymers60,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.189, 86.865, 91.830
Angle α, β, γ (deg.)75.720, 85.560, 85.280
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 138 or resid 140 through 522))
21(chain B and (resid 2 through 138 or resid 140 through 522))
31(chain C and (resid 2 through 138 or resid 140 through 522))
41(chain D and (resid 2 through 138 or resid 140 through 522))

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASN(chain A and (resid 2 through 138 or resid 140 through 522))AA2 - 13816 - 152
12LYSLYS(chain A and (resid 2 through 138 or resid 140 through 522))AA140 - 522154 - 534
21ASNASN(chain B and (resid 2 through 138 or resid 140 through 522))BB2 - 13816 - 152
22LYSLYS(chain B and (resid 2 through 138 or resid 140 through 522))BB140 - 522154 - 534
31ASNASN(chain C and (resid 2 through 138 or resid 140 through 522))CC2 - 13816 - 152
32LYSLYS(chain C and (resid 2 through 138 or resid 140 through 522))CC140 - 522154 - 534
41ASNASN(chain D and (resid 2 through 138 or resid 140 through 522))DD2 - 13816 - 152
42LYSLYS(chain D and (resid 2 through 138 or resid 140 through 522))DD140 - 522154 - 534

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Components

#1: Protein
iNicSnFR 3.0 Fluorescent Nicotine Sensor


Mass: 60329.359 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5% PEG 1,000 12.5% PEG 3,350 12.5% MPD 0.02 M of each amino acid 0.1 M MOPS/HEPES-Na, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9848 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9848 Å / Relative weight: 1
ReflectionResolution: 2.5→40.39 Å / Num. obs: 82648 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.03 Å2 / CC1/2: 0.978 / Rpim(I) all: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.5 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4588 / Rpim(I) all: 0.466 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S7T

7s7t


Resolution: 2.5→40.39 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.01
RfactorNum. reflection% reflection
Rfree0.2746 2004 2.43 %
Rwork0.2317 --
obs0.2327 82525 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.78 Å2 / Biso mean: 39.8669 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 2.5→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16134 0 0 512 16646
Biso mean---36.31 -
Num. residues----2034
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9781X-RAY DIFFRACTION13.451TORSIONAL
12B9781X-RAY DIFFRACTION13.451TORSIONAL
13C9781X-RAY DIFFRACTION13.451TORSIONAL
14D9781X-RAY DIFFRACTION13.451TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.37941380.31685476561493
2.56-2.630.32481410.29435756589798
2.63-2.710.36641320.2955734586698
2.71-2.790.37321470.27955754590198
2.79-2.890.35851480.27485736588498
2.89-3.010.33891500.26695743589398
3.01-3.150.34011360.26075756589299
3.15-3.310.33131430.24895763590699
3.31-3.520.29821500.24235813596399
3.52-3.790.28051440.23045773591799
3.79-4.170.21691440.21175767591199
4.17-4.770.20021430.18485819596299
4.77-6.010.24971430.20725796593999
6.01-40.390.2171450.20055835598099

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