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- PDB-5y0v: Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1... -

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Basic information

Entry
Database: PDB / ID: 5y0v
TitleCrystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with berberine
ComponentsBeta-hexosaminidaseHexosaminidase
KeywordsHYDROLASE / Ostrinia furnacalis / berberine
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / chitin catabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / lysosome / plasma membrane
Similarity search - Function
Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / 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
BERBERINE / Chitooligosaccharidolytic beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.423 Å
AuthorsDuan, Y.W. / Liu, T. / Tang, J.Y. / Li, M. / Yang, Q.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine.
Authors: Duan, Y. / Liu, T. / Zhou, Y. / Dou, T. / Yang, Q.
History
DepositionJul 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3654
Polymers66,3831
Non-polymers9823
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint12 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.821, 107.821, 175.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-hexosaminidase / Hexosaminidase


Mass: 66382.727 Da / Num. of mol.: 1 / Mutation: F243D,L570F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q06GJ0, beta-N-acetylhexosaminidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-BER / BERBERINE / Berberine


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 4.48 Å3/Da / Density % sol: 72.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100mM HEPES, 200mM MgCl2, 30% PEG 400, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 41233 / % possible obs: 99.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.034 / Rrim(I) all: 0.118 / Χ2: 0.965 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.42-2.4610.50.79222600.9470.2530.8330.798100
2.46-2.5110.70.6960.940.2210.7310.79100
2.51-2.5510.40.6070.9720.1960.6390.804100
2.55-2.6111.80.5770.970.1740.6040.807100
2.61-2.6612.60.5510.9740.1610.5740.803100
2.66-2.7312.60.470.9830.1370.490.809100
2.73-2.7912.60.4040.9850.1180.4220.847100
2.79-2.8712.40.3190.9870.0940.3330.88100
2.87-2.9512.30.2840.990.0850.2960.893100
2.95-3.0511.90.2420.9920.0730.2530.914100
3.05-3.1611.40.2040.9910.0630.2140.986100
3.16-3.2812.80.1680.9950.0490.1750.976100
3.28-3.43130.1360.9960.0390.1421.0999.9
3.43-3.6112.90.1160.9960.0340.1211.169100
3.61-3.8412.70.10.9970.0290.1051.212100
3.84-4.1411.50.0840.9960.0260.0881.23299.9
4.14-4.5512.70.0710.9980.0210.0741.18899.8
4.55-5.2112.70.0660.9980.0190.0681.06999.6
5.21-6.5611.90.0630.9960.0190.0660.89299.9
6.56-5011.30.070.9970.0220.0741.0399.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSM

3nsm


Resolution: 2.423→39.635 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.86
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2026 3463 4.82 %
Rwork0.1787 --
obs0.1799 41157 83.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.02 Å2 / Biso mean: 40.954 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 2.423→39.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 67 230 4912
Biso mean--79.46 41.41 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034817
X-RAY DIFFRACTIONf_angle_d0.5846553
X-RAY DIFFRACTIONf_chiral_restr0.043691
X-RAY DIFFRACTIONf_plane_restr0.003838
X-RAY DIFFRACTIONf_dihedral_angle_d8.4362845
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4233-2.45650.3516580.23961132119034
2.4565-2.49160.2429690.22731258132738
2.4916-2.52880.2842690.21211366143542
2.5288-2.56830.2502860.22151489157545
2.5683-2.61040.2574820.21711828191056
2.6104-2.65540.28681080.23052189229766
2.6554-2.70360.21241290.23942439256873
2.7036-2.75560.30851280.22612535266378
2.7556-2.81190.2221330.21982708284182
2.8119-2.8730.2611390.20722840297986
2.873-2.93980.28471440.21783017316191
2.9398-3.01330.22281680.20553137330596
3.0133-3.09470.24861630.21963226338999
3.0947-3.18580.20341640.213432893453100
3.1858-3.28850.25891740.209632453419100
3.2885-3.4060.26151610.191532983459100
3.406-3.54230.20221620.18232903452100
3.5423-3.70340.1981700.171133183488100
3.7034-3.89850.17861530.161732743427100
3.8985-4.14250.17521680.147433443512100
4.1425-4.4620.15461720.138832543426100
4.462-4.91020.15071680.139132763444100
4.9102-5.6190.15821600.153232613421100
5.619-7.07290.18151680.17332893457100
7.0729-39.64050.18961670.16733153332096

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