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- PDB-8u46: Crystal structure of Bacteroides thetaiotaomicron VPI-5482 Endogl... -

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Basic information

Entry
Database: PDB / ID: 8u46
TitleCrystal structure of Bacteroides thetaiotaomicron VPI-5482 Endoglycosidase BT1285 D161A-E163A inactive version
ComponentsEndo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / Endoglycosidase / artificial lectin / high mannose specific / Bacteroides
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Endo-beta-N-acetylglucosaminidase / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSastre, D.E. / Sultana, N. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM148075-01A1 United States
CitationJournal: Nat Commun / Year: 2024
Title: Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate.
Authors: Sastre, D.E. / Sultana, N. / V A S Navarro, M. / Huliciak, M. / Du, J. / Cifuente, J.O. / Flowers, M. / Liu, X. / Lollar, P. / Trastoy, B. / Guerin, M.E. / Sundberg, E.J.
History
DepositionSep 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase


Theoretical massNumber of molelcules
Total (without water)30,3541
Polymers30,3541
Non-polymers00
Water3,027168
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)70.309, 70.466, 50.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase


Mass: 30353.545 Da / Num. of mol.: 1 / Mutation: D161A, E163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1285 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8A889
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each divalent cation 0.1 M MOPS/HEPES-Na pH 7.5

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 14793 / % possible obs: 98.35 % / Redundancy: 6 % / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.057 / Rrim(I) all: 0.188 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6926 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.184 / Rrim(I) all: 0.57 / Χ2: 0.674 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 743 5.03 %
Rwork0.1608 --
obs0.1633 14781 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 0 168 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072052
X-RAY DIFFRACTIONf_angle_d0.8382796
X-RAY DIFFRACTIONf_dihedral_angle_d12.448287
X-RAY DIFFRACTIONf_chiral_restr0.057301
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.25871440.18392697X-RAY DIFFRACTION96
2.26-2.490.25131480.17872761X-RAY DIFFRACTION99
2.49-2.850.24621430.1762794X-RAY DIFFRACTION99
2.85-3.590.22871550.1612859X-RAY DIFFRACTION99
3.59-49.770.16561530.14422927X-RAY DIFFRACTION98

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