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- PDB-7s7x: Crystal structure of iCytSnFR Cytisine Sensor precursor binding p... -

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Basic information

Entry
Database: PDB / ID: 7s7x
TitleCrystal structure of iCytSnFR Cytisine Sensor precursor binding protein with varenicline bound
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 / homologyDI(HYDROXYETHYL)ETHER / VARENICLINE
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
B: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
C: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,67410
Polymers99,3123
Non-polymers1,3627
Water15,187843
1
A: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5223
Polymers33,1041
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6294
Polymers33,1041
Non-polymers5253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5223
Polymers33,1041
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.471, 99.910, 135.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 86 or resid 88...
21(chain C and (resid 1 through 86 or resid 88...
31(chain B and (resid 1 through 86 or resid 88...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 86 or resid 88...A1 - 86
121(chain A and (resid 1 through 86 or resid 88...A88 - 116
131(chain A and (resid 1 through 86 or resid 88...A1 - 301
141(chain A and (resid 1 through 86 or resid 88...A1 - 301
151(chain A and (resid 1 through 86 or resid 88...A123 - 156
161(chain A and (resid 1 through 86 or resid 88...A167 - 171
171(chain A and (resid 1 through 86 or resid 88...A1
181(chain A and (resid 1 through 86 or resid 88...A401
211(chain C and (resid 1 through 86 or resid 88...C1 - 86
221(chain C and (resid 1 through 86 or resid 88...C88 - 116
231(chain C and (resid 1 through 86 or resid 88...C118 - 120
241(chain C and (resid 1 through 86 or resid 88...C167 - 171
251(chain C and (resid 1 through 86 or resid 88...C9
261(chain C and (resid 1 through 86 or resid 88...C241 - 278
271(chain C and (resid 1 through 86 or resid 88...C1 - 278
281(chain C and (resid 1 through 86 or resid 88...C241 - 278
291(chain C and (resid 1 through 86 or resid 88...C301 - 401
311(chain B and (resid 1 through 86 or resid 88...B1 - 86
321(chain B and (resid 1 through 86 or resid 88...B88 - 116
331(chain B and (resid 1 through 86 or resid 88...B118 - 120
341(chain B and (resid 1 through 86 or resid 88...B123 - 156
351(chain B and (resid 1 through 86 or resid 88...B158 - 165
361(chain B and (resid 1 through 86 or resid 88...B167 - 171
371(chain B and (resid 1 through 86 or resid 88...B173 - 239
381(chain B and (resid 1 through 86 or resid 88...B241 - 278
391(chain B and (resid 1 through 86 or resid 88...B301 - 401

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Components

#1: Protein iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein


Mass: 33103.918 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: C13H13N3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, agonist*YM
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES, pH 9.5 20% PEG 8,000

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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 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.92 Å / Num. obs: 96997 / % possible obs: 99.71 % / Redundancy: 2 % / Biso Wilson estimate: 20.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03468 / Rpim(I) all: 0.03468 / Rrim(I) all: 0.04905 / Net I/σ(I): 8.23
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4629 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 9392 / CC1/2: 0.655 / CC star: 0.89 / Rpim(I) all: 0.4629 / Rrim(I) all: 0.6546 / % possible all: 98.54

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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: 1.7→37.92 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.33
RfactorNum. reflection% reflection
Rfree0.2078 2359 2.44 %
Rwork0.1701 --
obs0.171 96851 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.23 Å2 / Biso mean: 24.4515 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: final / Resolution: 1.7→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 94 843 7570
Biso mean--25.31 33.07 -
Num. residues----834
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2580X-RAY DIFFRACTION5.907TORSIONAL
12C2580X-RAY DIFFRACTION5.907TORSIONAL
13B2580X-RAY DIFFRACTION5.907TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.31011320.26635349548198
1.73-1.770.29211380.237954865624100
1.77-1.810.25071390.224455325671100
1.81-1.860.22111360.217254955631100
1.86-1.910.28861370.219454995636100
1.91-1.970.29131390.210755115650100
1.97-2.030.2571380.196555265664100
2.03-2.10.23551370.189155295666100
2.1-2.190.22061390.174555195658100
2.19-2.280.22971380.18355555693100
2.28-2.410.17811380.165955345672100
2.41-2.560.21331400.168655885728100
2.56-2.750.21011390.166955635702100
2.75-3.030.25451390.179956205759100
3.03-3.470.19351410.160656375778100
3.47-4.370.17371410.138956635804100
4.37-37.920.14991480.139558866034100

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