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- PDB-8u47: Crystal structure of Bacteroides thetaiotaomicron VPI-5482 Endogl... -

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Basic information

Entry
Database: PDB / ID: 8u47
TitleCrystal structure of Bacteroides thetaiotaomicron VPI-5482 Endoglycosidase BT1285
ComponentsEndo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / Glycosyl Hydrolase / GH18 family / Bacteroides / Endoglycosidase / High-Mannose N-glycan specific
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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6704
Polymers30,4561
Non-polymers2143
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.800, 68.727, 51.029
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: 30455.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1285 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A889
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 296 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: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 58683 / % possible obs: 94.93 % / Redundancy: 10.2 % / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.034 / Rrim(I) all: 0.116 / Χ2: 0.757 / Net I/σ(I): 11.1
Reflection shellResolution: 1.28→1.33 Å / Num. unique obs: 4203 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.158 / Rrim(I) all: 0.499 / Χ2: 0.4 / % possible all: 68.5

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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: 1.33→40.97 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2011 3.74 %
Rwork0.1801 --
obs0.1809 53763 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 11 240 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062074
X-RAY DIFFRACTIONf_angle_d0.8962828
X-RAY DIFFRACTIONf_dihedral_angle_d12.354289
X-RAY DIFFRACTIONf_chiral_restr0.091302
X-RAY DIFFRACTIONf_plane_restr0.006371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.39771310.35433295X-RAY DIFFRACTION88
1.36-1.40.28961380.30573500X-RAY DIFFRACTION93
1.4-1.440.30931340.27863665X-RAY DIFFRACTION97
1.44-1.490.30391470.24413734X-RAY DIFFRACTION99
1.49-1.540.23071450.20873773X-RAY DIFFRACTION100
1.54-1.60.23631450.19973767X-RAY DIFFRACTION100
1.6-1.680.20591460.17763784X-RAY DIFFRACTION100
1.68-1.760.19571480.1783801X-RAY DIFFRACTION100
1.76-1.870.23551470.17853760X-RAY DIFFRACTION100
1.87-2.020.20551460.16833804X-RAY DIFFRACTION99
2.02-2.220.17651450.16683766X-RAY DIFFRACTION98
2.22-2.540.20041460.17423745X-RAY DIFFRACTION97
2.54-3.20.20341430.17563614X-RAY DIFFRACTION93
3.21-40.970.1571500.1573744X-RAY DIFFRACTION92

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