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- PDB-5fd0: Streptomyces plicatus N-acetyl-beta-hexosaminidase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5fd0
TitleStreptomyces plicatus N-acetyl-beta-hexosaminidase in complex with NAGlucal
ComponentsB-N-acetylhexosaminidase
KeywordsHYDROLASE / Family 20 glycoside hydrolase / SpHex / GH20 / NAG-glucal / hexosaminidase / glycosidase inhibitor
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / lysosome / carbohydrate metabolic process / membrane
Similarity search - Function
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, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...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, bacterial type, N-terminal / Glycosyl hydrolase family 20, 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
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVadlamani, G. / Mark, B.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Cystic Fibrosis Canada Canada
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: N-Acetyl glycals are tight-binding and environmentally insensitive inhibitors of hexosaminidases.
Authors: Santana, A.G. / Vadlamani, G. / Mark, B.L. / Withers, S.G.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 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

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Assembly

Deposited unit
A: B-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9168
Polymers56,1271
Non-polymers7907
Water12,196677
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: B-N-acetylhexosaminidase
hetero molecules

A: B-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,83316
Polymers112,2542
Non-polymers1,57914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area3560 Å2
ΔGint-107 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.170, 133.170, 176.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

21A-1070-

HOH

31A-1115-

HOH

41A-1154-

HOH

51A-1161-

HOH

61A-1329-

HOH

Detailsmonomer according to gel filtration

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Components

#1: Protein B-N-acetylhexosaminidase


Mass: 56126.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces plicatus (bacteria) / Gene: hex / Plasmid: pET-3a / Details (production host): Ampicillin resistance / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O85361
#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 / 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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8M ammonium sulphate, 0.1M trisodium citrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→54.81 Å / Num. obs: 61567 / % possible obs: 98.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 23.06 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.3 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2236)refinement
Aimlessdata scaling
PHASERphasing
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HP4

1hp4


Resolution: 2→33.759 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1796 2000 3.26 %Random selection
Rwork0.1496 ---
obs0.1506 61441 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 2→33.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 47 677 4580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014032
X-RAY DIFFRACTIONf_angle_d1.0315516
X-RAY DIFFRACTIONf_dihedral_angle_d10.0862347
X-RAY DIFFRACTIONf_chiral_restr0.059582
X-RAY DIFFRACTIONf_plane_restr0.008721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2891340.22994009X-RAY DIFFRACTION94
2.05-2.10550.23881350.21194015X-RAY DIFFRACTION94
2.1055-2.16740.23121380.19164101X-RAY DIFFRACTION96
2.1674-2.23730.20871400.17844142X-RAY DIFFRACTION97
2.2373-2.31730.20981410.1634206X-RAY DIFFRACTION98
2.3173-2.410.18461430.1614248X-RAY DIFFRACTION99
2.41-2.51970.21241440.15194288X-RAY DIFFRACTION100
2.5197-2.65250.21281450.14854292X-RAY DIFFRACTION100
2.6525-2.81860.17521440.15084322X-RAY DIFFRACTION100
2.8186-3.03610.17571460.14254336X-RAY DIFFRACTION100
3.0361-3.34140.17761460.13744337X-RAY DIFFRACTION100
3.3414-3.82430.14061460.1264330X-RAY DIFFRACTION99
3.8243-4.8160.12551450.11464325X-RAY DIFFRACTION97
4.816-33.76340.1851530.16164490X-RAY DIFFRACTION96

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