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- PDB-7s7w: Crystal structure of iNicSnFR3a Nicotine Sensor precursor binding... -

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Basic information

Entry
Database: PDB / ID: 7s7w
TitleCrystal structure of iNicSnFR3a Nicotine Sensor precursor binding protein
ComponentsiNicSnFR 3.0 Fluorescent Nicotine Sensor precursor binding protein
KeywordsFLUORESCENT PROTEIN / nicotine / periplasmic binding protein / nicotine-binding protein / fluorescent sensor / pharmacokinetic sensor / CHOLINE-BINDING PROTEIN
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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
CitationJournal: Ph.D.Thesis,California Institute of Technology / Year: 2020
Title: Structure, Function, and Application of Bacterial ABC Transporters
Authors: Fan, C.
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.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: iNicSnFR 3.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1886
Polymers33,0341
Non-polymers1545
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.801, 61.215, 58.803
Angle α, β, γ (deg.)90.000, 100.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein iNicSnFR 3.0 Fluorescent Nicotine Sensor precursor binding protein


Mass: 33033.738 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium acetate 0.1 M BisTris, pH 6.5 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.1→34.13 Å / Num. obs: 114191 / % possible obs: 96.8 % / Redundancy: 7 % / Biso Wilson estimate: 13.98 Å2 / Rpim(I) all: 0.02 / Net I/σ(I): 14.1
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5453 / Rpim(I) all: 0.876 / Χ2: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
Blu-Icedata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S7T

7s7t


Resolution: 1.1→31.54 Å / SU ML: 0.1295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1982 2000 1.75 %
Rwork0.1728 112036 -
obs0.1732 114036 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.21 Å2
Refinement stepCycle: LAST / Resolution: 1.1→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 8 362 2632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422402
X-RAY DIFFRACTIONf_angle_d0.77013262
X-RAY DIFFRACTIONf_chiral_restr0.0786362
X-RAY DIFFRACTIONf_plane_restr0.0044421
X-RAY DIFFRACTIONf_dihedral_angle_d15.181918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.33981380.32397691X-RAY DIFFRACTION93.1
1.13-1.160.27921410.28957909X-RAY DIFFRACTION95.83
1.16-1.190.28931410.26157948X-RAY DIFFRACTION96.08
1.19-1.230.23171420.23677958X-RAY DIFFRACTION96.01
1.23-1.270.27761380.2127705X-RAY DIFFRACTION93.56
1.27-1.320.19991440.19128023X-RAY DIFFRACTION97.08
1.32-1.390.18311420.17828024X-RAY DIFFRACTION96.96
1.39-1.460.19681450.16278083X-RAY DIFFRACTION97.44
1.46-1.550.1561430.15018012X-RAY DIFFRACTION96.59
1.55-1.670.17861420.1467968X-RAY DIFFRACTION96.15
1.67-1.840.17971460.15918177X-RAY DIFFRACTION98.52
1.84-2.10.17711460.16918187X-RAY DIFFRACTION98.41
2.1-2.650.20421440.17398090X-RAY DIFFRACTION96.96
2.65-31.540.19431480.168261X-RAY DIFFRACTION97.95

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