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- PDB-6je8: crystal structure of a beta-N-acetylhexosaminidase -

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Basic information

Entry
Database: PDB / ID: 6je8
Titlecrystal structure of a beta-N-acetylhexosaminidase
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Catalyze / acetamidodeoxyhexohydrolase
Function / homology
Function and homology information


chitobiose catabolic process / beta-N-acetylgalactosaminidase activity / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / metal ion binding / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Beta-hexosaminidase Amuc_2018
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)54,2008
Polymers53,6281
Non-polymers5727
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-2 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.422, 84.345, 92.447
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


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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
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: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50339 / % possible obs: 98.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Χ2: 0.917 / Net I/σ(I): 11.7 / Num. measured all: 303267
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.864.80.50847050.8510.2460.5670.78393.4
1.86-1.946.30.38850140.9370.1640.4220.85199.5
1.94-2.036.40.29250110.9610.1230.3170.88899.6
2.03-2.136.40.22649990.9720.0950.2450.94399.1
2.13-2.276.20.17950290.9790.0770.1960.98399.2
2.27-2.445.80.14450150.9840.0640.1580.9799
2.44-2.696.40.11650900.9890.050.1270.90299.9
2.69-3.086.20.0950810.9930.0390.0980.92899.3
3.08-3.885.70.06850730.9960.030.0740.96797.9
3.88-505.90.05653220.9960.0250.0610.92498.8

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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: 1.798→46.224 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 2484 4.94 %
Rwork0.1433 47797 -
obs0.145 50281 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.22 Å2 / Biso mean: 19.8126 Å2 / Biso min: 4.59 Å2
Refinement stepCycle: final / Resolution: 1.798→46.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 37 621 4434
Biso mean--33.98 31.86 -
Num. residues----469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.798-1.83260.22651140.18872271238585
1.8326-1.870.22151430.17332593273697
1.87-1.91070.2251420.154326302772100
1.9107-1.95510.19231320.14826712803100
1.9551-2.0040.18481520.144726392791100
2.004-2.05820.1811180.138326892807100
2.0582-2.11870.19381630.14332599276299
2.1187-2.18710.18151290.14592681281099
2.1871-2.26530.19861480.14482641278999
2.2653-2.3560.17791340.14732646278099
2.356-2.46320.2051380.14842697283599
2.4632-2.59310.18661330.150226802813100
2.5931-2.75550.18381420.150627012843100
2.7555-2.96820.18891310.14872713284499
2.9682-3.26690.17771260.15012682280898
3.2669-3.73940.15021530.13342647280097
3.7394-4.71050.15231440.115627612905100
4.7105-46.23880.15091420.14782856299898

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