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- PDB-7cbn: Crystal structure of beta-N-acetylhexosaminidase Am0868 from Akke... -

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Basic information

Entry
Database: PDB / ID: 7cbn
TitleCrystal structure of beta-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Akkermansia muciniphila / beta-N-acetylhexosaminidases / Mucin degradation
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / polysaccharide catabolic process / 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
MALONIC ACID / Beta-hexosaminidase Amuc_0868
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXu, W. / Wang, M. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentKJ2019ZD02 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural and biochemical analyses of beta-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila involved in mucin degradation.
Authors: Xu, W. / Yang, W. / Wang, Y. / Wang, M. / Zhang, M.
History
DepositionJun 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4354
Polymers61,1351
Non-polymers3003
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-3 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.584, 72.435, 137.727
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: 61135.008 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_0868 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UQG6, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.24 M sodium malonate pH 7.0 and 20% Polyethylene glycol 3350

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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: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 61817 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Χ2: 0.978 / Net I/σ(I): 9.3 / Num. measured all: 734909
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7610.40.83360920.8580.2680.8760.984100
1.76-1.8312.50.55961110.9440.1630.5830.915100
1.83-1.9111.60.45661060.9360.1410.4781.1799.9
1.91-2.0211.70.32761090.9730.10.3421.141100
2.02-2.1411.80.22660980.9740.070.2371.03599.9
2.14-2.3111.30.17661360.9870.0550.1841.05699.8
2.31-2.5412.80.12261820.9960.0360.1280.891100
2.54-2.9112.10.08961900.9970.0270.0930.906100
2.91-3.6612.40.06362670.9980.0190.0650.905100
3.66-5012.20.04565260.9990.0130.0470.82799.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q63

6q63


Resolution: 1.7→38.777 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1848 3170 5.14 %
Rwork0.1534 58510 -
obs0.155 61680 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.1 Å2 / Biso mean: 24.3724 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 1.7→38.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 20 725 4941
Biso mean--31.13 35.68 -
Num. residues----526
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72520.25711370.2147229091
1.7252-1.75220.22421500.18332505100
1.7522-1.78090.2271420.17582491100
1.7809-1.81160.2311540.16772529100
1.8116-1.84460.24711150.16482519100
1.8446-1.88010.23361470.16872528100
1.8801-1.91840.2841200.2142254999
1.9184-1.96010.23791410.18972501100
1.9601-2.00570.20241420.16392525100
2.0057-2.05590.1741490.152538100
2.0559-2.11150.21911130.1804251499
2.1115-2.17360.19581280.1532568100
2.1736-2.24370.19481450.1652532100
2.2437-2.32390.23421600.1795251999
2.3239-2.4170.18511270.15672554100
2.417-2.52690.17731430.16082545100
2.5269-2.66010.19471120.15862585100
2.6601-2.82680.21291180.15832572100
2.8268-3.04490.20071460.15152582100
3.0449-3.35120.17121590.14872555100
3.3512-3.83580.15591420.13052612100
3.8358-4.83120.14391320.11682643100
4.8312-38.770.14541480.1516275499

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