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- PDB-7wdt: 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifid... -

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Basic information

Entry
Database: PDB / ID: 7wdt
Title6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / Glycoside Hydrolase family 20
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-NGS / Chem-NGY / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBifidobacterium bifidum JCM 1254 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsYamada, C. / Kashima, T. / Fushinobu, S. / Katoh, T. / Katayama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K05789 Japan
Japan Society for the Promotion of Science (JSPS)21H02116 Japan
Citation
Journal: Nat.Chem.Biol. / Year: 2023
Title: A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Authors: Katoh, T. / Yamada, C. / Wallace, M.D. / Yoshida, A. / Gotoh, A. / Arai, M. / Maeshibu, T. / Kashima, T. / Hagenbeek, A. / Ojima, M.N. / Takada, H. / Sakanaka, M. / Shimizu, H. / Nishiyama, ...Authors: Katoh, T. / Yamada, C. / Wallace, M.D. / Yoshida, A. / Gotoh, A. / Arai, M. / Maeshibu, T. / Kashima, T. / Hagenbeek, A. / Ojima, M.N. / Takada, H. / Sakanaka, M. / Shimizu, H. / Nishiyama, K. / Ashida, H. / Hirose, J. / Suarez-Diez, M. / Nishiyama, M. / Kimura, I. / Stubbs, K.A. / Fushinobu, S. / Katayama, T.
#1: Journal: Biosci Biotechnol Biochem / Year: 2017
Title: Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization.
Authors: Katoh, T. / Maeshibu, T. / Kikkawa, K.I. / Gotoh, A. / Tomabechi, Y. / Nakamura, M. / Liao, W.H. / Yamaguchi, M. / Ashida, H. / Yamamoto, K. / Katayama, T.
History
DepositionDec 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4214
Polymers89,7781
Non-polymers6433
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.131, 57.879, 98.530
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 89778.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria)
Gene: bbhII / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): delta-lacZ-CodonPlus / References: UniProt: D4QAP5, beta-N-acetylhexosaminidase
#2: Sugar ChemComp-NGS / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-SULFATE / N-acetyl-6-O-sulfo-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAc[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-NGY / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / N-acetyl-6-O-sulfo-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, alpha linking / Mass: 301.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAc[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% (w/v) PEG 8000, 0.1 M HEPES-NaOH (pH 7.5) and 5 mM GlcNAc-6S

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 8, 2018
RadiationMonochromator: fixed exit Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.76 Å / Num. obs: 104324 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.063 / Net I/σ(I): 10.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.975 / Num. unique obs: 5063 / CC1/2: 0.72 / Rpim(I) all: 0.779 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→48.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.294 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 5253 5 %RANDOM
Rwork0.1697 ---
obs0.1712 99053 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.47 Å2 / Biso mean: 20.26 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0 Å2-1.91 Å2
2--0.11 Å2-0 Å2
3---1.61 Å2
Refinement stepCycle: final / Resolution: 1.65→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 0 39 619 6897
Biso mean--22.92 26.71 -
Num. residues----819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136416
X-RAY DIFFRACTIONr_bond_other_d0.0020.0155820
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6418752
X-RAY DIFFRACTIONr_angle_other_deg1.5241.57813408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37123.206315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93715995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8961531
X-RAY DIFFRACTIONr_chiral_restr0.080.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027397
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021449
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 387 -
Rwork0.28 7203 -
all-7590 -
obs--98.71 %

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