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- PDB-7s7y: Crystal structure of iCytSnFR Cytisine Sensor precursor binding p... -

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Basic information

Entry
Database: PDB / ID: 7s7y
TitleCrystal structure of iCytSnFR Cytisine Sensor precursor binding protein
ComponentsiNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
KeywordsFLUORESCENT PROTEIN / nicotine / gfp / periplasmic binding protein / nicotine-binding protein / fluorescent sensor / pharmacokinetic sensor / CHOLINE-BINDING PROTEIN
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFan, C. / Nichols, N.L. / Luebbert, L. / 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1732
Polymers33,1041
Non-polymers691
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.688, 61.100, 58.546
Angle α, β, γ (deg.)90.000, 100.640, 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 4.0 Fluorescent Nicotine Sensor precursor binding protein


Mass: 33103.918 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 8,000 3% MPD 0.1 M Imidazole, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→34.03 Å / Num. obs: 69428 / % possible obs: 97.64 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.21 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05284 / Rpim(I) all: 0.02157 / Rrim(I) all: 0.05717 / Net I/σ(I): 14.22
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 6 % / Rmerge(I) obs: 1.381 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 6647 / CC1/2: 0.743 / CC star: 0.923 / Rpim(I) all: 0.5986 / Rrim(I) all: 1.51 / % possible all: 94.27

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Processing

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

7s7t


Resolution: 1.3→34.03 Å / SU ML: 0.1593 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8265
RfactorNum. reflection% reflection
Rfree0.2019 2000 2.89 %
Rwork0.1802 --
obs0.1808 69273 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.86 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 5 249 2469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472307
X-RAY DIFFRACTIONf_angle_d0.75973129
X-RAY DIFFRACTIONf_chiral_restr0.0769350
X-RAY DIFFRACTIONf_plane_restr0.0052399
X-RAY DIFFRACTIONf_dihedral_angle_d13.111867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.44141340.3864508X-RAY DIFFRACTION92.65
1.33-1.370.35041400.31884721X-RAY DIFFRACTION96.62
1.37-1.410.31341430.27464794X-RAY DIFFRACTION98.01
1.41-1.450.2731440.24194831X-RAY DIFFRACTION97.88
1.45-1.510.25551420.21914778X-RAY DIFFRACTION97.66
1.51-1.570.21611410.19134749X-RAY DIFFRACTION96.34
1.57-1.640.19511430.16694810X-RAY DIFFRACTION98.47
1.64-1.720.2231460.16394898X-RAY DIFFRACTION98.9
1.72-1.830.20911440.17274835X-RAY DIFFRACTION98.77
1.83-1.970.20741420.1894780X-RAY DIFFRACTION96.87
1.97-2.170.2131450.17664897X-RAY DIFFRACTION99.15
2.17-2.490.2151450.18154876X-RAY DIFFRACTION98.86
2.49-3.130.21151430.18824837X-RAY DIFFRACTION97.72
3.13-34.030.16321480.15574959X-RAY DIFFRACTION98.4

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