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- PDB-1m01: Wildtype Streptomyces plicatus beta-hexosaminidase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1m01
TitleWildtype Streptomyces plicatus beta-hexosaminidase in complex with product (GlcNAc)
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / substrate assisted catalysis / streptomyces plicatus / hexosaminidase / TIM barrel
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / 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 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; 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 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / 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
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsJ Williams, S. / Mark, B.L. / Vocadlo, D.J. / James, M.N.G. / Withers, S.G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state.
Authors: Williams, S.J. / Mark, B.L. / Vocadlo, D.J. / James, M.N. / Withers, S.G.
History
DepositionJun 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: 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_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 375SPECIAL POSITION THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS OF A SYMMETRY RELATED ...SPECIAL POSITION THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL POSITIONS. ATOM RES CSSEQI CL CL 307 LIES ON A SPECIAL POSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8279
Polymers56,1271
Non-polymers7008
Water5,044280
1


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

A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,65318
Polymers112,2542
Non-polymers1,40016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6810 Å2
ΔGint-113 kcal/mol
Surface area32030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.276, 133.276, 176.204
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-510-

CL

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-N-acetylhexosaminidase / beta-hexosaminidase / SpHEX


Mass: 56126.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces plicatus (bacteria) / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O85361, 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
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

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Non-polymers , 4 types, 287 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.02 Å3/Da / Density % sol: 69.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM SULFATE, TRI-SODIUM CITRATE, GLYCEROL, GlcNAc, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mMtrisodium citrate1drop
2300 mM1dropNaCl
310 mg/mlprotein1drop
42.1 Mammonium sulfate1reservoir
5100 mMtrisodium citrate1reservoirpH6.0
620 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→70 Å / Num. all: 54264 / Num. obs: 54264 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.038 / Net I/σ(I): 39.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 12 % / Mean I/σ(I) obs: 15.1 / Num. unique all: 2604 / Rsym value: 0.1 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 70 Å / Num. measured all: 747643 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 97.4 % / Num. unique obs: 2604 / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1HP4

1hp4


Resolution: 2.1→70 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5466 10.1 %RANDOM
Rwork0.195 ---
obs0.195 54204 99.6 %-
all-54204 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0292 Å2 / ksol: 0.386255 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20.91 Å20 Å2
2--1.99 Å20 Å2
3----3.97 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 41 280 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 866 9.9 %
Rwork0.199 7900 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2IFG_GOL.PARIFG_GOL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBONAG.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 70 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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