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- PDB-6per: Crystal Structure of Ligand-Free iSeroSnFR -

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Basic information

Entry
Database: PDB / ID: 6per
TitleCrystal Structure of Ligand-Free iSeroSnFR
ComponentsiSeroSnFR, a soluble, genetically-encoded fluorescent sensor for serotonin
KeywordsFLUORESCENT PROTEIN / fluorescent sensor / serotonin binding protein / biosensor
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHartanto, S. / Tian, L. / Fisher, A.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)U01NS090604 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5U01NS103522-02 United States
National Institutes of Health/Office of the Director1DP2MH107056 United States
CitationJournal: Cell / Year: 2020
Title: Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.
Authors: Unger, E.K. / Keller, J.P. / Altermatt, M. / Liang, R. / Matsui, A. / Dong, C. / Hon, O.J. / Yao, Z. / Sun, J. / Banala, S. / Flanigan, M.E. / Jaffe, D.A. / Hartanto, S. / Carlen, J. / ...Authors: Unger, E.K. / Keller, J.P. / Altermatt, M. / Liang, R. / Matsui, A. / Dong, C. / Hon, O.J. / Yao, Z. / Sun, J. / Banala, S. / Flanigan, M.E. / Jaffe, D.A. / Hartanto, S. / Carlen, J. / Mizuno, G.O. / Borden, P.M. / Shivange, A.V. / Cameron, L.P. / Sinning, S. / Underhill, S.M. / Olson, D.E. / Amara, S.G. / Temple Lang, D. / Rudnick, G. / Marvin, J.S. / Lavis, L.D. / Lester, H.A. / Alvarez, V.A. / Fisher, A.J. / Prescher, J.A. / Kash, T.L. / Yarov-Yarovoy, V. / Gradinaru, V. / Looger, L.L. / Tian, L.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 1.3Nov 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: iSeroSnFR, a soluble, genetically-encoded fluorescent sensor for serotonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5716
Polymers62,2601
Non-polymers3105
Water4,053225
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)80.672, 99.255, 150.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein iSeroSnFR, a soluble, genetically-encoded fluorescent sensor for serotonin


Mass: 62260.477 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)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.4 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES:NaOH, 30% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2017
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→82.87 Å / Num. obs: 34793 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2 / Num. unique obs: 2849 / CC1/2: 0.682 / Rpim(I) all: 0.414 / Rrim(I) all: 0.765 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSQ, 4Z7E

3osq

4z7e


Resolution: 2.1→62.602 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 3284 5.17 %Random selection
Rwork0.1879 ---
obs0.1902 63535 93.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→62.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 20 225 4259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084126
X-RAY DIFFRACTIONf_angle_d1.0735575
X-RAY DIFFRACTIONf_dihedral_angle_d4.9293467
X-RAY DIFFRACTIONf_chiral_restr0.06614
X-RAY DIFFRACTIONf_plane_restr0.006724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13140.29461320.26762613X-RAY DIFFRACTION94
2.1314-2.16470.29421480.26032677X-RAY DIFFRACTION95
2.1647-2.20020.29581540.25572689X-RAY DIFFRACTION95
2.2002-2.23810.36541410.25422644X-RAY DIFFRACTION94
2.2381-2.27880.2641480.25332567X-RAY DIFFRACTION92
2.2788-2.32260.31891220.2452590X-RAY DIFFRACTION91
2.3226-2.370.26081330.22552707X-RAY DIFFRACTION95
2.37-2.42160.28531430.23032645X-RAY DIFFRACTION95
2.4216-2.47790.32381560.22032638X-RAY DIFFRACTION95
2.4779-2.53990.2661500.21072694X-RAY DIFFRACTION95
2.5399-2.60850.26711550.2062665X-RAY DIFFRACTION95
2.6085-2.68530.24021590.19762598X-RAY DIFFRACTION94
2.6853-2.7720.26261510.1952589X-RAY DIFFRACTION93
2.772-2.87110.19911160.18312600X-RAY DIFFRACTION91
2.8711-2.9860.22311430.17882705X-RAY DIFFRACTION95
2.986-3.12190.21981130.18022672X-RAY DIFFRACTION94
3.1219-3.28650.23991360.1842652X-RAY DIFFRACTION93
3.2865-3.49240.21971530.17492588X-RAY DIFFRACTION93
3.4924-3.7620.19231270.1712530X-RAY DIFFRACTION90
3.762-4.14050.20641520.17092584X-RAY DIFFRACTION92
4.1405-4.73950.17281450.14632624X-RAY DIFFRACTION92
4.7395-5.97050.2581660.1762456X-RAY DIFFRACTION89
5.9705-62.630.19691410.17342524X-RAY DIFFRACTION89

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