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- PDB-7s80: Crystal structure of iAChSnFR Acetylcholine Sensor precursor bind... -

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Basic information

Entry
Database: PDB / ID: 7s80
TitleCrystal structure of iAChSnFR Acetylcholine Sensor precursor binding protein
ComponentsiAchSnFR Fluorescent Acetylcholine Sensor precursor binding protein
KeywordsFLUORESCENT PROTEIN / Acetylcholine / periplasmic binding protein / nicotine-binding protein / fluorescent sensor / pharmacokinetic sensor / CHOLINE-BINDING PROTEIN
Function / homologyMALONATE ION
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFan, C. / Borden, P.M. / 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: iAchSnFR Fluorescent Acetylcholine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1653
Polymers33,0011
Non-polymers1642
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.536, 60.816, 58.657
Angle α, β, γ (deg.)90.000, 100.519, 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 iAchSnFR Fluorescent Acetylcholine Sensor precursor binding protein


Mass: 33000.836 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 44.27 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% PEG 1,500 0.1M MIB, pH 5.0

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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: Jun 20, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.9 Å / Num. obs: 55565 / % possible obs: 98.09 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.36 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06134 / Rpim(I) all: 0.02555 / Rrim(I) all: 0.06659 / Net I/σ(I): 12.83
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.209 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 5503 / CC1/2: 0.776 / CC star: 0.935 / Rpim(I) all: 0.504 / Rrim(I) all: 1.312 / % possible all: 97.79

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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: 1.4→33.9 Å / SU ML: 0.1475 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8006
RfactorNum. reflection% reflection
Rfree0.1953 2000 3.6 %
Rwork0.1696 --
obs0.1705 55498 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.06 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 11 171 2394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452303
X-RAY DIFFRACTIONf_angle_d0.74633124
X-RAY DIFFRACTIONf_chiral_restr0.0743353
X-RAY DIFFRACTIONf_plane_restr0.0052400
X-RAY DIFFRACTIONf_dihedral_angle_d13.2848865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.35381410.32113779X-RAY DIFFRACTION96.84
1.43-1.470.28751420.28523805X-RAY DIFFRACTION98.48
1.47-1.520.24941440.23383804X-RAY DIFFRACTION97.82
1.52-1.570.24941400.23763X-RAY DIFFRACTION97.53
1.57-1.620.22721380.18313687X-RAY DIFFRACTION95.1
1.62-1.690.19641440.15833862X-RAY DIFFRACTION99.16
1.69-1.760.19051440.16023835X-RAY DIFFRACTION99.08
1.76-1.860.22021430.17293831X-RAY DIFFRACTION98.54
1.86-1.970.24281420.17783820X-RAY DIFFRACTION97.71
1.97-2.120.19891410.16713780X-RAY DIFFRACTION97.56
2.13-2.340.2111460.16813896X-RAY DIFFRACTION99.36
2.34-2.680.20591440.17773840X-RAY DIFFRACTION98.69
2.68-3.370.18441430.18453858X-RAY DIFFRACTION98.16
3.37-33.90.16731480.14473938X-RAY DIFFRACTION98.81

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