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- PDB-8fxt: Escherichia coli periplasmic Glucose-Binding Protein glucose comp... -

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Basic information

Entry
Database: PDB / ID: 8fxt
TitleEscherichia coli periplasmic Glucose-Binding Protein glucose complex: Acrylodan conjugate attached at W183C
ComponentsD-galactose/methyl-galactoside binding periplasmic protein MglB
KeywordsSUGAR BINDING PROTEIN / Periplasmic binding protein / Biosensor Fluorescent conjugate
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding / metal ion binding
Similarity search - Function
D-galactose-binding periplasmic protein MglB-like, PBP domain / : / Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-D-glucopyranose / 1-[6-(dimethylamino)naphthalen-2-yl]propan-1-one / D-galactose/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsAllert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Becton-Dickinson and Company United States
CitationJournal: Commun Chem / Year: 2023
Title: Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching.
Authors: Allert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W.
History
DepositionJan 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Derived calculations / Category: struct_conn
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-galactose/methyl-galactoside binding periplasmic protein MglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2129
Polymers32,8641
Non-polymers1,3488
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.587, 36.533, 79.905
Angle α, β, γ (deg.)90.000, 124.130, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

21A-813-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein D-galactose/methyl-galactoside binding periplasmic protein MglB


Mass: 32864.027 Da / Num. of mol.: 1 / Mutation: W183C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mglB / Production host: Escherichia coli (E. coli) / References: UniProt: E2QP16

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Sugars , 2 types, 6 molecules

#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 320 molecules

#2: Chemical ChemComp-YDM / 1-[6-(dimethylamino)naphthalen-2-yl]propan-1-one / acrylodan, bound form


Mass: 227.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 43030 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.57 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Net I/σ(I): 25.54
Reflection shellResolution: 1.53→1.56 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.99 / Num. unique obs: 2019 / Rpim(I) all: 0.131

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→24.75 Å / SU ML: 0.149 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.3363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1826 1999 4.68 %
Rwork0.1555 40707 -
obs0.1568 42706 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.98 Å2
Refinement stepCycle: LAST / Resolution: 1.53→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 90 318 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01372488
X-RAY DIFFRACTIONf_angle_d1.28813383
X-RAY DIFFRACTIONf_chiral_restr0.2499400
X-RAY DIFFRACTIONf_plane_restr0.0096434
X-RAY DIFFRACTIONf_dihedral_angle_d13.6253900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.2711050.19952141X-RAY DIFFRACTION72.33
1.56-1.60.20791370.18032776X-RAY DIFFRACTION93.52
1.6-1.650.21661410.16852889X-RAY DIFFRACTION97.49
1.65-1.710.2281430.17752914X-RAY DIFFRACTION99.06
1.71-1.770.19911440.17412939X-RAY DIFFRACTION98.44
1.77-1.840.23591470.17062985X-RAY DIFFRACTION99.11
1.84-1.920.20051440.16032950X-RAY DIFFRACTION99.68
1.92-2.020.20211480.15772997X-RAY DIFFRACTION99.75
2.02-2.150.17531470.15422974X-RAY DIFFRACTION99.49
2.15-2.310.17011460.14492994X-RAY DIFFRACTION99.87
2.31-2.550.15661460.15252969X-RAY DIFFRACTION99.9
2.55-2.910.18561490.15333033X-RAY DIFFRACTION99.94
2.91-3.670.17421500.14493050X-RAY DIFFRACTION99.97
3.67-24.750.15681520.14873096X-RAY DIFFRACTION99.57

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