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- PDB-6v1r: Crystal structure of iAChSnFR Fluorescent Acetylcholine Sensor pr... -

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Basic information

Entry
Database: PDB / ID: 6v1r
TitleCrystal structure of iAChSnFR Fluorescent Acetylcholine Sensor precursor binding protein
ComponentsiAChSnFR Fluorescent Acetylcholine Sensor V9 precursor binding protein
KeywordsNeurotransmitter-binding protein
Function / homologyABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ACETYLCHOLINE / DI(HYDROXYETHYL)ETHER / SPERMIDINE / Glycine/betaine ABC transporter substrate-binding protein
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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, DA043829, GM123582 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)
Tobacco-Related Disease Research Program (TRDRP)23XT-0007 United States
Tobacco-Related Disease Research Program (TRDRP)27IP-0057 United States
CitationJournal: To Be Published
Title: A genetically encoded fluorescent sensor for in vivo acetylcholine detection
Authors: Borden, P.M. / Shivange, A.V. / Fan, C. / Rees, D.C. / Lester, H.A. / Looger, L.L.
History
DepositionNov 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iAChSnFR Fluorescent Acetylcholine Sensor V9 precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6065
Polymers33,0011
Non-polymers6054
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.760, 65.781, 96.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein iAChSnFR Fluorescent Acetylcholine Sensor V9 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) / References: UniProt: A0A3B8MYE1*PLUS

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter*YM
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 20% PEG 8,000 0.1 M CHES, pH 9.5 10 mM spermidine

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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: 1.64→38.11 Å / Num. obs: 36549 / % possible obs: 98.88 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06946 / Rpim(I) all: 0.02968 / Rrim(I) all: 0.0757 / Net I/σ(I): 13.18
Reflection shellResolution: 1.645→1.704 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.257 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 3406 / CC1/2: 0.636 / Rpim(I) all: 0.5266 / Rrim(I) all: 1.366 / % possible all: 93.98

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EFR

6efr


Resolution: 1.64→38.11 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 1828 5 %
Rwork0.18 34705 -
obs0.182 36533 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.94 Å2
Refinement stepCycle: LAST / Resolution: 1.64→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 40 206 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612366
X-RAY DIFFRACTIONf_angle_d0.86283209
X-RAY DIFFRACTIONf_chiral_restr0.053358
X-RAY DIFFRACTIONf_plane_restr0.0052409
X-RAY DIFFRACTIONf_dihedral_angle_d9.678336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.33141280.28482428X-RAY DIFFRACTION92.17
1.69-1.740.27631400.23822652X-RAY DIFFRACTION99.29
1.74-1.80.27731410.22482656X-RAY DIFFRACTION99.43
1.8-1.860.24991370.22142613X-RAY DIFFRACTION99.1
1.86-1.930.31961400.25692670X-RAY DIFFRACTION99.36
1.93-2.020.22941400.20712669X-RAY DIFFRACTION99.61
2.02-2.130.2261400.18782669X-RAY DIFFRACTION99.65
2.13-2.260.23851390.19652630X-RAY DIFFRACTION99.25
2.26-2.440.22151430.18452712X-RAY DIFFRACTION99.44
2.44-2.680.20131410.1792687X-RAY DIFFRACTION99.82
2.68-3.070.24961420.18272704X-RAY DIFFRACTION99.3
3.07-3.870.19631460.16742755X-RAY DIFFRACTION99.86
3.87-38.110.19451510.14742860X-RAY DIFFRACTION99.21
Refinement TLS params.Method: refined / Origin x: 1.25788693607 Å / Origin y: 5.52090573478 Å / Origin z: 30.1156423022 Å
111213212223313233
T0.187484514176 Å20.0146725305107 Å2-0.0185436250012 Å2-0.184692575139 Å2-0.011472153515 Å2--0.167359766931 Å2
L1.94862551756 °20.375866278707 °2-0.710607712865 °2-1.66632439913 °2-0.214425747934 °2--0.856743584609 °2
S-0.0629188838565 Å °0.0107927524019 Å °0.0157216223243 Å °-0.0363078038021 Å °0.0518985335941 Å °-0.0815420943357 Å °0.0416274733147 Å °-0.0337578546016 Å °0.00256179183796 Å °
Refinement TLS groupSelection details: all

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