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- PDB-7vi6: Crystal structure of GH3 beta-N-acetylhexosaminidase Amuc_2109 fr... -

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Basic information

Entry
Database: PDB / ID: 7vi6
TitleCrystal structure of GH3 beta-N-acetylhexosaminidase Amuc_2109 from Akkermansia muciniphila
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Akkermansia muciniphila / beta-N-acetylhexosaminidases / GH3 / Catalytic mechanism.
Function / homology
Function and homology information


peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsQian, K. / Yang, W. / Chen, X. / Wang, Y. / Zhang, M. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentKJ2019ZD02 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Functional and structural characterization of a GH3 beta-N-acetylhexosaminidase from Akkermansia muciniphila involved in mucin degradation
Authors: Qian, K. / Yang, W. / Chen, X. / Wang, Y. / Zhang, M. / Wang, M.
History
DepositionSep 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,43517
Polymers78,9582
Non-polymers47615
Water9,008500
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7058
Polymers39,4791
Non-polymers2267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7299
Polymers39,4791
Non-polymers2508
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.926, 81.105, 126.991
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: 39479.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc) (bacteria)
Gene: Amuc_2109 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2UPP0, beta-N-acetylhexosaminidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2M NaCl, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 55774 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.056 / Rrim(I) all: 0.136 / Χ2: 1.136 / Net I/σ(I): 6.3 / Num. measured all: 353083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.076.70.88155060.870.3750.9591.185100
2.07-2.156.70.70154950.8840.2920.761.066100
2.15-2.256.50.49155390.90.2140.5361.182100
2.25-2.376.30.41854960.9350.1810.4561.30999.9
2.37-2.526.80.28655250.9660.120.3111.19299.9
2.52-2.716.50.22155630.9710.0950.2411.186100
2.71-2.996.30.15955710.9830.070.1741.05199.9
2.99-3.426.30.1255840.9880.0530.1311.09499.8
3.42-4.315.80.0956340.990.0420.11.07399.7
4.31-505.50.07858610.9930.0380.0870.99499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZM6

4zm6


Resolution: 2→39.46 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 2776 4.99 %
Rwork0.1834 52848 -
obs0.1855 55624 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.92 Å2 / Biso mean: 43.0295 Å2 / Biso min: 24.53 Å2
Refinement stepCycle: final / Resolution: 2→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 15 500 5718
Biso mean--51.98 48.55 -
Num. residues----682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.29431590.24952568272799
2.03-2.070.34831370.29062582271999
2.07-2.110.28581330.258225932726100
2.11-2.150.24621530.221526152768100
2.15-2.20.28151270.217326302757100
2.2-2.250.32841400.27152616275699
2.25-2.310.33881350.266526082743100
2.31-2.370.27341320.20926252757100
2.37-2.440.22461310.20126262757100
2.44-2.520.2481070.204826532760100
2.52-2.610.26441620.200226292791100
2.61-2.710.25281360.202726322768100
2.71-2.840.271350.202126392774100
2.84-2.990.2331290.194126632792100
2.99-3.170.24981480.196626302778100
3.17-3.420.21581450.177426552800100
3.42-3.760.17951540.156226642818100
3.76-4.310.17171310.141226792810100
4.31-5.420.20421320.14822717284999
5.42-39.460.20471500.17782824297499

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