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

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Basic information

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


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / polysaccharide catabolic process
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_0868
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5444
Polymers61,1351
Non-polymers4093
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-10 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.231, 72.132, 138.228
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 / Plasmid: p28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UQG6, 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M AmSO4, 0.1 M MES pH 6.0, 20% PEG 3350

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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 / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 86352 / % possible obs: 96.8 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.043 / Rrim(I) all: 0.152 / Χ2: 0.919 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5512.50.98681910.7310.2861.0280.62993.4
1.55-1.6211.80.79182920.8010.2350.8270.70794.3
1.62-1.6912.70.66184510.8370.1910.6890.79295.6
1.69-1.7812.50.54285110.8940.1590.5650.996.3
1.78-1.8911.80.40785430.9330.1230.4261.0696.8
1.89-2.0412.20.30386520.9680.0910.3171.20397.4
2.04-2.2412.20.2286940.9820.0660.231.29197.8
2.24-2.56120.14287840.9910.0430.1491.01698.3
2.56-3.23130.10189350.9950.0290.1050.9198.9
3.23-5012.40.06592990.9980.0190.0670.6999.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CBN

7cbn


Resolution: 1.5→27.08 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1728 4187 5.13 %
Rwork0.1408 77391 -
obs0.1424 81578 91.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.85 Å2 / Biso mean: 20.0632 Å2 / Biso min: 7.03 Å2
Refinement stepCycle: final / Resolution: 1.5→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4156 0 26 802 4984
Biso mean--20.86 34.67 -
Num. residues----522
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.51540.2146940.1845150254
1.5154-1.53320.21981010.1781180064
1.5332-1.55190.2424970.1743196171
1.5519-1.57160.24941260.1747207074
1.5716-1.59230.19141280.1731224080
1.5923-1.61410.21461160.1656225782
1.6141-1.63710.20461080.1635245287
1.6371-1.66160.24321400.1712253590
1.6616-1.68750.21681330.1732252490
1.6875-1.71520.1981520.1645257692
1.7152-1.74480.22441560.1633261094
1.7448-1.77650.2361520.1725265995
1.7765-1.81060.17661500.1682265996
1.8106-1.84760.21521390.1764271296
1.8476-1.88780.22331400.1732271096
1.8878-1.93170.19451440.1569271997
1.9317-1.97990.19081500.1542271997
1.9799-2.03350.1871680.1488273098
2.0335-2.09330.17211300.153276798
2.0933-2.16080.18781310.1514276898
2.1608-2.2380.18351540.1452275698
2.238-2.32760.17521730.1361276698
2.3276-2.43340.16921390.1371277999
2.4334-2.56160.17591440.1388279898
2.5616-2.7220.18761300.137282699
2.722-2.93190.17321510.131284999
2.9319-3.22660.15881660.1255283599
3.2266-3.69240.14871660.1128284799
3.6924-4.64830.12451480.1044291799
4.6483-27.080.12651610.13983048100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8586-0.12810.08821.97510.4331.608-0.02070.2287-0.28410.01850.04980.09820.2748-0.1108-0.03680.1372-0.0568-0.03570.1443-0.01160.1724-0.3956-6.929846.3782
20.30270.0968-0.07510.4075-0.19140.40270.0253-0.0083-0.01420.04510.0061-0.0166-0.0004-0.0049-0.03060.09090.0013-0.01050.0891-0.00610.083720.696119.285451.5157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 147 )A27 - 147
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 548 )A148 - 548

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