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- PDB-8u9f: Crystal structure of Bacteroides thetaiotamicron BT1285 in comple... -

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Basic information

Entry
Database: PDB / ID: 8u9f
TitleCrystal structure of Bacteroides thetaiotamicron BT1285 in complex with NaI
ComponentsEndo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / Endoglycosidase / ENGase / GH18 family / Bacteroides thetaiotaomicron / I-SAD
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
IODIDE ION / Endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.08 Å
AuthorsSastre, D.E. / Navarro, M.V.A.S. / 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 19, 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
Revision 1.2Dec 25, 2024Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn / Item: _pdbx_entry_details.has_protein_modification

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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)33,83332
Polymers30,4561
Non-polymers3,37831
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.540, 70.005, 70.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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 (bacteria) / References: UniProt: Q8A889
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.08→41.5 Å / Num. obs: 191890 / % possible obs: 90.8 % / Redundancy: 3 % / CC1/2: 0.997 / Net I/σ(I): 11.5
Reflection shellResolution: 1.08→1.14 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 17229 / CC1/2: 0.921 / % possible all: 50.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.08→41.5 Å / SU ML: 0.06 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 10.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1274 9575 4.99 %
Rwork0.1112 --
obs0.112 191874 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.08→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 52 357 2476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122324
X-RAY DIFFRACTIONf_angle_d1.3333182
X-RAY DIFFRACTIONf_dihedral_angle_d12.024345
X-RAY DIFFRACTIONf_chiral_restr0.113340
X-RAY DIFFRACTIONf_plane_restr0.01427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.3258390.2304692X-RAY DIFFRACTION10
1.09-1.10.24551210.20292439X-RAY DIFFRACTION36
1.1-1.120.19452030.17793875X-RAY DIFFRACTION57
1.12-1.130.19432570.15244846X-RAY DIFFRACTION73
1.13-1.150.15672810.13575411X-RAY DIFFRACTION81
1.15-1.160.16263020.12985802X-RAY DIFFRACTION87
1.16-1.180.12543200.12476228X-RAY DIFFRACTION93
1.18-1.20.13083350.12096416X-RAY DIFFRACTION96
1.2-1.210.12633430.11366604X-RAY DIFFRACTION99
1.21-1.230.1453520.10866698X-RAY DIFFRACTION100
1.23-1.260.13653520.10326701X-RAY DIFFRACTION100
1.26-1.280.1233530.10056630X-RAY DIFFRACTION100
1.28-1.30.12893570.10016683X-RAY DIFFRACTION100
1.3-1.330.11443520.09726667X-RAY DIFFRACTION100
1.33-1.360.1233560.0976716X-RAY DIFFRACTION100
1.36-1.390.1243450.09696595X-RAY DIFFRACTION100
1.39-1.430.11823500.09556704X-RAY DIFFRACTION100
1.43-1.460.12623600.08966666X-RAY DIFFRACTION100
1.46-1.510.10223520.08496696X-RAY DIFFRACTION100
1.51-1.560.10353540.08336719X-RAY DIFFRACTION100
1.56-1.610.10593430.0866647X-RAY DIFFRACTION100
1.61-1.680.11823480.08756659X-RAY DIFFRACTION100
1.68-1.750.1033520.09346660X-RAY DIFFRACTION100
1.75-1.840.11383500.09636669X-RAY DIFFRACTION99
1.84-1.960.10863450.09476612X-RAY DIFFRACTION99
1.96-2.110.11393510.10126696X-RAY DIFFRACTION100
2.11-2.320.12993450.10396643X-RAY DIFFRACTION100
2.32-2.660.12943520.11466661X-RAY DIFFRACTION99
2.66-3.350.12763450.13056625X-RAY DIFFRACTION99
3.35-41.50.14653600.14056639X-RAY DIFFRACTION99

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