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- PDB-6dgv: iGABASnFR Fluorescent GABA Sensor precursor -

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Basic information

Entry
Database: PDB / ID: 6dgv
TitleiGABASnFR Fluorescent GABA Sensor precursor
ComponentsFluorescent GABA Sensor precursor
KeywordsFLUORESCENT PROTEIN / GABA binding protein / Fluorescent sensor / Superfolder / Circularly permuted GFP / Periplasmic binding protein
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ABC transporter substrate-binding protein
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMarvin, J.S. / Looger, L.L.
CitationJournal: Nat.Methods / Year: 2019
Title: A genetically encoded fluorescent sensor for in vivo imaging of GABA.
Authors: Marvin, J.S. / Shimoda, Y. / Magloire, V. / Leite, M. / Kawashima, T. / Jensen, T.P. / Kolb, I. / Knott, E.L. / Novak, O. / Podgorski, K. / Leidenheimer, N.J. / Rusakov, D.A. / Ahrens, M.B. ...Authors: Marvin, J.S. / Shimoda, Y. / Magloire, V. / Leite, M. / Kawashima, T. / Jensen, T.P. / Kolb, I. / Knott, E.L. / Novak, O. / Podgorski, K. / Leidenheimer, N.J. / Rusakov, D.A. / Ahrens, M.B. / Kullmann, D.M. / Looger, L.L.
History
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent GABA Sensor precursor


Theoretical massNumber of molelcules
Total (without water)62,6331
Polymers62,6331
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.970, 160.970, 50.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Fluorescent GABA Sensor precursor


Mass: 62633.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B3D787*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.056 M Sodium phosphate monobasic monohydrate 1.344 M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→139.404 Å / Num. obs: 18621 / % possible obs: 100 % / Redundancy: 21.5 % / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.08 / Rrim(I) all: 0.37 / Net I/σ(I): 14.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.025 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2692 / Rpim(I) all: 0.549 / Rrim(I) all: 2.56 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQ7 and the cpGFP component of 3OSR

4eq7

3osr


Resolution: 2.8→139.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.075 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 1.644 / ESU R Free: 0.321 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 927 5 %RANDOM
Rwork0.17512 ---
obs0.17777 17682 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.432 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→139.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 0 6 4321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194420
X-RAY DIFFRACTIONr_bond_other_d0.0020.024151
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9545994
X-RAY DIFFRACTIONr_angle_other_deg1.01839568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4985550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85725.224201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83215723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215056
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021007
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2994.7162209
X-RAY DIFFRACTIONr_mcbond_other3.2974.7162208
X-RAY DIFFRACTIONr_mcangle_it4.9457.0662756
X-RAY DIFFRACTIONr_mcangle_other4.9447.0672757
X-RAY DIFFRACTIONr_scbond_it4.0585.0572211
X-RAY DIFFRACTIONr_scbond_other4.0575.0572212
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4217.3853239
X-RAY DIFFRACTIONr_long_range_B_refined8.06936.9524778
X-RAY DIFFRACTIONr_long_range_B_other8.06836.9584779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 70 -
Rwork0.284 1288 -
obs--100 %

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