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- PDB-8tde: Structure of glucose bound Bacteroides thetaiotaomicron 3-Keto-2-... -

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Basic information

Entry
Database: PDB / ID: 8tde
TitleStructure of glucose bound Bacteroides thetaiotaomicron 3-Keto-2-hydroxy-glucal-hydratase BT2
ComponentsProbable secreted glycosyl hydrolase
KeywordsISOMERASE / Hydratase / GH16-like
Function / homology3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / alpha-D-glucopyranose / : / Probable secreted glycosyl hydrolase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nature / Year: 2024
Title: An alternative broad-specificity pathway for glycan breakdown in bacteria
Authors: Nasseri, S.A. / Lazarski, A.C. / Lemmer, I.L. / Zhang, C.Y. / Brencher, E. / Chen, H. / Sim, L. / Panwar, D. / Betschart, L. / Worrall, L.J. / Brumer, H. / Strynadka, N.C.J. / Withers, S.G.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable secreted glycosyl hydrolase
B: Probable secreted glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1805
Polymers62,9222
Non-polymers2583
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.037, 81.171, 103.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable secreted glycosyl hydrolase


Mass: 31460.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A5T1
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Citrate 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1807 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2023
RadiationMonochromator: 1.18 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1807 Å / Relative weight: 1
ReflectionResolution: 1.85→43.72 Å / Num. obs: 56186 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 0.95 / Net I/σ(I): 11.5 / Num. measured all: 343709
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 1.365 / Num. measured all: 22575 / Num. unique obs: 3456 / CC1/2: 0.588 / Rpim(I) all: 0.572 / Rrim(I) all: 1.483 / Χ2: 0.8 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3osd

3osd


Resolution: 1.85→43.72 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2296 --
Rwork0.1915 --
obs-56120 99.76 %
Refinement stepCycle: LAST / Resolution: 1.85→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 14 404 4476

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