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- PDB-3vtr: Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1... -

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Basic information

Entry
Database: PDB / ID: 3vtr
TitleCrystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 E328A complexed with TMG-chitotriomycin
ComponentsN-acetylglucosaminidase
KeywordsHYDROLASE/ANTIBIOTIC / insect / chitin / beta-N-acetyl-D-hexosaminidase / TMG-chitotriomycin / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


glycosaminoglycan metabolic process / ganglioside catabolic process / beta-N-acetylhexosaminidase / : / 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
TMG-chitotriomycin / Chitooligosaccharidolytic beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, T. / Zhou, Y. / Chen, L. / Chen, W. / Liu, L. / Shen, X. / Yang, Q.
CitationJournal: Plos One / Year: 2012
Title: Structural insights into cellulolytic and chitinolytic enzymes revealing crucial residues of insect beta-N-acetyl-D-hexosaminidase
Authors: Liu, T. / Zhou, Y. / Chen, L. / Chen, W. / Liu, L. / Shen, X. / Zhang, W. / Zhang, J. / Yang, Q.
History
DepositionJun 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7694
Polymers65,4951
Non-polymers1,2743
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylglucosaminidase
hetero molecules

A: N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5388
Polymers130,9902
Non-polymers2,5496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area8160 Å2
ΔGint-20 kcal/mol
Surface area39520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.937, 107.937, 174.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein N-acetylglucosaminidase / beta-N-acetyl-D-hexosaminidase


Mass: 65494.812 Da / Num. of mol.: 1 / Fragment: residues 23-594 / Mutation: E328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Pichia pastoris (fungus) / References: UniProt: Q06GJ0, beta-N-acetylhexosaminidase
#2: Polysaccharide 2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / TMG-chitotriomycin


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 831.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: TMG-chitotriomycin
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NC/2C/2C]/1-1-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Glcp2NDiMe]{}}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100MM HEPES, 200MM MGCL2, 33% PEG 400, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→53.97 Å / Num. obs: 41167 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.22 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.376 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
PHENIX1.8_1069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSN

3nsn


Resolution: 2.5→49.477 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU ML: 0.26 / σ(F): 1.37 / Phase error: 27.97 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.244 2070 5.04 %
Rwork0.217 --
obs0.2184 41052 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.277 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å21.67 Å20 Å2
2--3.35 Å20 Å2
3----5.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 85 254 4950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094827
X-RAY DIFFRACTIONf_angle_d1.1376554
X-RAY DIFFRACTIONf_dihedral_angle_d15.6961745
X-RAY DIFFRACTIONf_chiral_restr0.09704
X-RAY DIFFRACTIONf_plane_restr0.004835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.55830.31811350.27342529X-RAY DIFFRACTION98
2.5583-2.62220.30671460.25842537X-RAY DIFFRACTION98
2.6222-2.69310.29251200.27812584X-RAY DIFFRACTION98
2.6931-2.77240.31121390.26722545X-RAY DIFFRACTION99
2.7724-2.86180.28411230.23452579X-RAY DIFFRACTION99
2.8618-2.96410.24711510.23282545X-RAY DIFFRACTION99
2.9641-3.08280.27711540.25012544X-RAY DIFFRACTION99
3.0828-3.2230.26511380.24242580X-RAY DIFFRACTION99
3.223-3.39290.3041320.24682588X-RAY DIFFRACTION99
3.3929-3.60550.22371480.23082617X-RAY DIFFRACTION99
3.6055-3.88370.27461390.23542602X-RAY DIFFRACTION100
3.8837-4.27440.2291520.19922612X-RAY DIFFRACTION100
4.2744-4.89240.21841380.17482657X-RAY DIFFRACTION100
4.8924-6.16210.21321310.19312663X-RAY DIFFRACTION100
6.1621-49.48690.19671240.19942800X-RAY DIFFRACTION99

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