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- PDB-8fxu: Thermoanaerobacter thermosaccharolyticum periplasmic Glucose-Bind... -

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Basic information

Entry
Database: PDB / ID: 8fxu
TitleThermoanaerobacter thermosaccharolyticum periplasmic Glucose-Binding Protein glucose complex: Badan conjugate attached at F17C
ComponentsD-galactose/methyl-galactoside binding periplasmic protein MglB
KeywordsSUGAR BINDING PROTEIN / Periplasmic binding protein / Biosensor Fluorescent conjugate
Function / homologybeta-D-glucopyranose / : / Chem-YDQ
Function and homology information
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsAllert, M.J. / Kumar, S. / Beese, L.S. / Hellinga, H.W.
Funding support1items
OrganizationGrant numberCountry
Other private
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 1.1Oct 16, 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

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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)34,8997
Polymers34,2771
Non-polymers6226
Water7,026390
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)45.490, 53.060, 134.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 34276.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum (bacteria)
Gene: Thert_00913
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / 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 , 5 types, 395 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-YDQ / 2-bromo-1-[6-(dimethylamino)naphthalen-2-yl]ethan-1-one / BADAN


Mass: 292.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14BrNO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→37.66 Å / Num. obs: 44519 / % possible obs: 99.83 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.08522 / Rpim(I) all: 0.034 / Net I/σ(I): 16.44
Reflection shellResolution: 1.59→1.647 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.7435 / Num. unique obs: 4304 / Rpim(I) all: 0.2944 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→37.66 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.3857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 2044 4.59 %
Rwork0.1608 42473 -
obs0.1616 44517 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 1.59→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 32 390 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132555
X-RAY DIFFRACTIONf_angle_d1.14633474
X-RAY DIFFRACTIONf_chiral_restr0.1337384
X-RAY DIFFRACTIONf_plane_restr0.005454
X-RAY DIFFRACTIONf_dihedral_angle_d13.544952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.29921330.24222752X-RAY DIFFRACTION98.1
1.63-1.670.27811330.20692756X-RAY DIFFRACTION100
1.67-1.710.21271350.18752803X-RAY DIFFRACTION99.97
1.71-1.760.19021350.1762794X-RAY DIFFRACTION100
1.76-1.820.20141360.16922813X-RAY DIFFRACTION100
1.82-1.890.18481340.16742793X-RAY DIFFRACTION99.97
1.89-1.960.20081350.16892799X-RAY DIFFRACTION100
1.96-2.050.19591360.16422813X-RAY DIFFRACTION100
2.05-2.160.1751360.15592824X-RAY DIFFRACTION99.97
2.16-2.290.17361360.15412823X-RAY DIFFRACTION100
2.29-2.470.18021360.15632816X-RAY DIFFRACTION100
2.47-2.720.19421370.15962858X-RAY DIFFRACTION99.97
2.72-3.110.15711390.16432876X-RAY DIFFRACTION99.87
3.11-3.920.16011400.14832899X-RAY DIFFRACTION99.97
3.92-37.660.14691430.14833054X-RAY DIFFRACTION99.81

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