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- PDB-6jea: crystal structure of a beta-N-acetylhexosaminidase -

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Basic information

Entry
Database: PDB / ID: 6jea
Titlecrystal structure of a beta-N-acetylhexosaminidase
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / Catalyze / acetamidodeoxyhexohydrolase
Function / homology
Function and homology information


chitobiose catabolic process / beta-N-acetylgalactosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / metal ion binding
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-hexosaminidase Amuc_2018
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.275 Å
AuthorsChen, X. / Wang, J.C. / Liu, M.J. / Yang, W.Y. / Wang, Y.Z. / Tang, R.P. / Zhang, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystallographic evidence for substrate-assisted catalysis of beta-N-acetylhexosaminidas from Akkermansia muciniphila.
Authors: Chen, X. / Wang, J. / Liu, M. / Yang, W. / Wang, Y. / Tang, R. / Zhang, M.
History
DepositionFeb 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9153
Polymers53,6281
Non-polymers2872
Water6,305350
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)68.555, 83.309, 91.350
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 Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 53628.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2018
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B2UP57, beta-N-acetylhexosaminidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.1M Sodium malonate, pH 7.0; 0.1 M HEPES pH 7.0; 0.5%v/v Jeffamine ED-2001 pH 7.0 and 0.2 M sodium formate; 20% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24175 / % possible obs: 99.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.081 / Rrim(I) all: 0.19 / Χ2: 1.066 / Net I/σ(I): 4 / Num. measured all: 130566
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.385.40.95123790.550.4511.0570.934100
2.38-2.485.20.78123870.6620.380.8730.93899.8
2.48-2.595.40.60923530.7410.290.6770.95698.7
2.59-2.735.60.55323890.770.2560.6121.14399.8
2.73-2.95.60.36124070.8950.1680.40.96899.8
2.9-3.125.50.2624010.9470.1220.289199.8
3.12-3.445.30.16523940.9780.0780.1831.06198.9
3.44-3.935.60.13324370.980.0620.1481.35899.7
3.93-4.955.20.08324600.9940.0390.0921.15998.9
4.95-505.20.07325680.9940.0340.0811.11398.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCN

3rcn


Resolution: 2.275→38.011 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 1230 5.1 %
Rwork0.168 22902 -
obs0.1703 24132 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.13 Å2 / Biso mean: 35.0123 Å2 / Biso min: 18.45 Å2
Refinement stepCycle: final / Resolution: 2.275→38.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 16 350 4142
Biso mean--33.91 38.18 -
Num. residues----469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2754-2.36640.32821130.24572199231286
2.3664-2.47410.27521460.224325452691100
2.4741-2.60450.26331250.21082540266599
2.6045-2.76770.25281430.21525612704100
2.7677-2.98130.26181410.199525592700100
2.9813-3.28120.25151300.187725862716100
3.2812-3.75560.2111410.15842573271499
3.7556-4.73020.17271460.12752618276499
4.7302-38.01640.16081450.13352721286699

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