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- PDB-9fbu: X-ray structure of the iGluSnFR3 in complex with L-glutamate -

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Basic information

Entry
Database: PDB / ID: 9fbu
TitleX-ray structure of the iGluSnFR3 in complex with L-glutamate
ComponentsPeriplasmic binding transport protein,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / genetically-encoded biosensor / glutamate / iGluSnFR3 / GFP
Function / homology
Function and homology information


amino acid transport / bioluminescence / generation of precursor metabolites and energy / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
: / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
GLUTAMIC ACID / Periplasmic binding transport protein / Green fluorescent protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTarnawski, M. / Hiblot, J. / Leippe, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: X-ray structure of the iGluSnFR3 in complex with L-glutamate
Authors: Tarnawski, M. / Hiblot, J. / Leippe, P.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic binding transport protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1772
Polymers58,0291
Non-polymers1471
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.760, 100.840, 73.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1022-

HOH

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Components

#1: Protein Periplasmic binding transport protein,Green fluorescent protein


Mass: 58029.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ybeJ, SF0626, GFP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UXX1, UniProt: P42212
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 26% (m/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 6, 2023
RadiationMonochromator: S1(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 56404 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 8736 / CC1/2: 0.809 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.54 Å / SU ML: 0.1849 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 2820 5 %
Rwork0.1828 53581 -
obs0.1842 56401 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.81 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 10 334 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744100
X-RAY DIFFRACTIONf_angle_d0.92075541
X-RAY DIFFRACTIONf_chiral_restr0.062610
X-RAY DIFFRACTIONf_plane_restr0.0089731
X-RAY DIFFRACTIONf_dihedral_angle_d5.8908559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.33461390.2542638X-RAY DIFFRACTION98.86
1.73-1.760.27351400.23252652X-RAY DIFFRACTION98.9
1.76-1.790.26711380.22182626X-RAY DIFFRACTION98.96
1.79-1.830.26821380.21732627X-RAY DIFFRACTION98.86
1.83-1.870.24411390.20762635X-RAY DIFFRACTION99.14
1.87-1.910.24221390.21622646X-RAY DIFFRACTION99.39
1.91-1.960.24541390.2112645X-RAY DIFFRACTION99.43
1.96-2.020.24071400.2012643X-RAY DIFFRACTION99.22
2.02-2.070.28161400.1972659X-RAY DIFFRACTION99.4
2.07-2.140.26391410.19292689X-RAY DIFFRACTION99.51
2.14-2.220.21231400.19152657X-RAY DIFFRACTION99.57
2.22-2.310.25411400.19982667X-RAY DIFFRACTION99.61
2.31-2.410.23021410.19862668X-RAY DIFFRACTION99.68
2.41-2.540.23211410.19682693X-RAY DIFFRACTION99.44
2.54-2.70.23911410.19392671X-RAY DIFFRACTION99.4
2.7-2.910.20221430.19412706X-RAY DIFFRACTION99.58
2.91-3.20.18261410.18342698X-RAY DIFFRACTION99.61
3.2-3.660.19451450.17432737X-RAY DIFFRACTION99.62
3.66-4.610.1731440.14642749X-RAY DIFFRACTION99.04
4.61-41.540.16551510.15672875X-RAY DIFFRACTION99.21

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