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- PDB-6uru: iAChSnFR Fluorescent Acetylcholine Sensor precursor -

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Basic information

Entry
Database: PDB / ID: 6uru
TitleiAChSnFR Fluorescent Acetylcholine Sensor precursor
ComponentsiAChSnFR precursor
KeywordsFLUORESCENT PROTEIN / Biosensor / sensor / neurotransmitter / acetylcholine / circularly permuted
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBorden, P.M. / Marvin, J.S. / Looger, L.L.
CitationJournal: To Be Published
Title: iAChSnFR Fluorescent Acetylcholine Sensor precursor
Authors: Borden, P.M. / Marvin, J.S. / Looger, L.L.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iAChSnFR precursor
B: iAChSnFR precursor


Theoretical massNumber of molelcules
Total (without water)125,7942
Polymers125,7942
Non-polymers00
Water00
1
A: iAChSnFR precursor


Theoretical massNumber of molelcules
Total (without water)62,8971
Polymers62,8971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: iAChSnFR precursor


Theoretical massNumber of molelcules
Total (without water)62,8971
Polymers62,8971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.120, 89.780, 92.890
Angle α, β, γ (deg.)90.000, 90.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein iAChSnFR precursor


Mass: 62896.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Phosphate buffer

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→92.9 Å / Num. obs: 36373 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 1.228 / Num. unique obs: 5167 / CC1/2: 0.299

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f9g, 3ppn

5f9g

3ppn


Resolution: 2.6→92.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.025 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.976 / ESU R Free: 0.337
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1724 4.7 %RANDOM
Rwork0.2135 ---
obs0.2159 34575 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 177.77 Å2 / Biso mean: 53.719 Å2 / Biso min: 26.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.07 Å2
2--0.46 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 2.6→92.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 3370 0 11344
Biso mean--50.22 --
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0158148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177518
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.75511016
X-RAY DIFFRACTIONr_angle_other_deg0.4881.71217624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4885994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88821.825252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.807151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2281522
X-RAY DIFFRACTIONr_chiral_restr0.0580.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021462
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 105 -
Rwork0.333 2486 -
all-2591 -
obs--95.86 %

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