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- PDB-8tda: Structure of Bacteroides thetaiotaomicron 3-Keto-2-hydroxy-glucal... -

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Basic information

Entry
Database: PDB / ID: 8tda
TitleStructure of Bacteroides thetaiotaomicron 3-Keto-2-hydroxy-glucal-hydratase BT2
ComponentsProbable secreted glycosyl hydrolase
KeywordsISOMERASE / Hydratase / GH16-like
Function / homologyalpha-3'-ketoglucosidase / 3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / hydrolase activity, acting on glycosyl bonds / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / : / 3-keto-disaccharide hydrolase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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.M. / 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
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 2024Group: 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

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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)63,0786
Polymers62,9222
Non-polymers1564
Water9,854547
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.939, 80.018, 103.148
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: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Citrate 18% 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: 1.1808 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.46→61.15 Å / Num. obs: 109389 / % possible obs: 99.87 % / Redundancy: 6.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Net I/σ(I): 9.04
Reflection shellResolution: 1.46→1.512 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.223 / Num. unique obs: 10839 / CC1/2: 0.561 / Rpim(I) all: 0.549 / Rrim(I) all: 1.343

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→61.15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2125 --
Rwork0.1757 --
obs-109389 99.87 %
Refinement stepCycle: LAST / Resolution: 1.46→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 4 547 4605

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