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- PDB-7nwf: Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in c... -

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Basic information

Entry
Database: PDB / ID: 7nwf
TitleCrystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with hybrid-type glycan (GalGlcNAcMan5GlcNAc) product
ComponentsEndo-beta-N-acetylglucosaminidase F1
KeywordsHYDROLASE / endo-b-N-acetylglucosaminidase / EndoBT-3987 / BT3987 / glycoside hydrolase
Function / homologyDomain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / metal ion binding / Endo-beta-N-acetylglucosaminidase F1
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTrastoy, B. / Du, J.J. / Garcia-Alija, M. / Sundberg, E.J. / Guerin, M.E.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: GH18 endo-beta-N-acetylglucosaminidases use distinct mechanisms to process hybrid-type N-linked glycans.
Authors: Trastoy, B. / Du, J.J. / Li, C. / Garcia-Alija, M. / Klontz, E.H. / Roberts, B.R. / Donahue, T.C. / Wang, L.X. / Sundberg, E.J. / Guerin, M.E.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / diffrn_source / pdbx_database_proc / pdbx_entity_branch_descriptor
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7754
Polymers49,1941
Non-polymers1,5813
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint29 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.299, 74.024, 125.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase F1


Mass: 49193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3987 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A0N4
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-2-3-1-4-3-3-3/a4-b1_b3-c1_b6-f1_c2-d1_d4-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane 7.5, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→45.9 Å / Num. obs: 195095 / % possible obs: 95.06 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.51 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.11 / Net I/σ(I): 12.58
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 15200 / CC1/2: 0.85 / CC star: 0.96 / Rrim(I) all: 0.68 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3POH

3poh


Resolution: 2→45.888 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 1483 4.9 %
Rwork0.1833 28758 -
obs0.1847 30241 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.19 Å2 / Biso mean: 25.6705 Å2 / Biso min: 13.46 Å2
Refinement stepCycle: final / Resolution: 2→45.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 107 237 3606
Biso mean--32.24 26.84 -
Num. residues----432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06460.27161140.23372275100
2.0646-2.13840.28211090.2193227399
2.1384-2.2240.27191620.20992694100
2.224-2.32520.24771000.2075209677
2.3252-2.44780.20531350.19652726100
2.4478-2.60110.24751270.20722753100
2.6011-2.80190.24251340.20152736100
2.8019-3.08380.23741420.20112760100
3.0838-3.52990.21411590.18682739100
3.5299-4.44680.19011510.14822784100
4.4468-45.8880.15471500.1547292299

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