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- PDB-7bwg: A Glycoside Hydrolase Family 20 beta-N-Acetylglucosaminidase -

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Basic information

Entry
Database: PDB / ID: 7bwg
TitleA Glycoside Hydrolase Family 20 beta-N-Acetylglucosaminidase
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Glycoside Hydrolase Family 20 / beta-N-Acetylglucosaminidase / High Activity / Salt Tolerance
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesMicrobacterium sp. HJ5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhang, R. / Zhou, J.P. / Huang, Z.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31460694 China
CitationJournal: To Be Published
Title: A Glycoside Hydrolase Family 20 beta-Acetylglucosaminidase
Authors: Zhang, R. / Zhou, J.P. / Huang, Z.X.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 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
B: Beta-N-acetylhexosaminidase


Theoretical massNumber of molelcules
Total (without water)111,9242
Polymers111,9242
Non-polymers00
Water32418
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)78.035, 81.928, 79.418
Angle α, β, γ (deg.)90.000, 94.076, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 55961.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. HJ5 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6AQA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 10% (V/V) Dioxane, 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.848→57.61 Å / Num. obs: 23477 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.02 Å2 / CC1/2: 0.982 / CC star: 0.996 / Rmerge(I) obs: 0.2292 / Rrim(I) all: 0.2515 / Net I/σ(I): 8.19
Reflection shellResolution: 2.848→2.95 Å / Rmerge(I) obs: 0.7734 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 2334 / CC1/2: 0.864 / CC star: 0.963 / Rrim(I) all: 0.8446 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DENZOdata reduction
HKL-2000data scaling
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HP4

1hp4


Resolution: 2.85→57.61 Å / SU ML: 0.5058 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.0939 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3345 1190 5.07 %
Rwork0.2921 22276 -
obs0.2942 23466 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.72 Å2
Refinement stepCycle: LAST / Resolution: 2.85→57.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6602 0 0 18 6620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296774
X-RAY DIFFRACTIONf_angle_d0.64229313
X-RAY DIFFRACTIONf_chiral_restr0.04171078
X-RAY DIFFRACTIONf_plane_restr0.00771220
X-RAY DIFFRACTIONf_dihedral_angle_d3.41173876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.980.38611530.33282770X-RAY DIFFRACTION99.9
2.98-3.130.41261250.36092797X-RAY DIFFRACTION99.86
3.13-3.330.37871250.34032760X-RAY DIFFRACTION99.28
3.33-3.590.38761610.33122778X-RAY DIFFRACTION99.86
3.59-3.950.34831830.31122738X-RAY DIFFRACTION99.69
3.95-4.520.31521410.25962794X-RAY DIFFRACTION99.73
4.52-5.690.2931540.24782802X-RAY DIFFRACTION99.7
5.69-57.610.25011480.23742837X-RAY DIFFRACTION99.04

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