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- PDB-1hp5: STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1hp5
TitleSTREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE COMPLEXED WITH INTERMEDIATE ANALOUGE NAG-THIAZOLINE
ComponentsBETA-N-ACETYLHEXOSAMINIDASE
KeywordsHYDROLASE / glycosyl hydrolase / streptomyces plicatus / hexosaminidase / family 20 / substrate assisted catalysis / 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
Chem-NGT / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 2.1 Å
AuthorsMark, B.L.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase.
Authors: Mark, B.L. / Vocadlo, D.J. / Knapp, S. / Triggs-Raine, B.L. / Withers, S.G. / James, M.N.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Structural and Functional Characterization of Streptomyces plicatus Beta-N-acetylhexosaminidase by Comparative Molecular Modeling and Site-directed Mutagenesis
Authors: Mark, B.L. / Wasney, G.A. / Salo, T.J. / Khan, A.R. / Cao, Z. / Robbins, P.W. / James, M.N. / Triggs-Raine, B.L.
#2: Journal: J.Am.Chem.Soc. / Year: 1996
Title: NAG-thiazoline, An N-acetyl-betahexosaminidase inhibitor that implicates acetamido participation
Authors: Knapp, S. / Vocadlo, D. / Gao, Z. / Kirk, B. / Lou, J. / Withers, S.G.
#3: Journal: Gene / Year: 1992
Title: Cloning and high-level expression of a chitinase-encoding gene of Streptomyces plicatus
Authors: Robbins, P.W. / Overbye, K. / Albright, C. / Benfield, B. / Pero, J.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Cloning and expression of a Streptomyces plicatus chitinase (chitinase-63) in Escherichia coli
Authors: Robbins, P.W. / Albright, C. / Benfield, B.
History
DepositionDec 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Aug 9, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)56,7338
Polymers56,1271
Non-polymers6067
Water4,864270
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)113,46516
Polymers112,2542
Non-polymers1,21214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5620 Å2
ΔGint-93 kcal/mol
Surface area32590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.621, 133.621, 174.194
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-509-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA-N-ACETYLHEXOSAMINIDASE


Mass: 56126.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces plicatus (bacteria) / Plasmid: PET3A(P3AHEX-1.8) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O85361, beta-N-acetylhexosaminidase

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Non-polymers , 5 types, 277 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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 Å3/Da / Density % sol: 69.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, tri-sodium citrate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.2 Mammonium sulfate1reservoir
3100 mMtrisodium citrate1reservoirpH6.0
420-25 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2000
Details: Flat collimating mirror; double crystal Si(111) monochromator; toroid mirror (vertical and horizontal focusing)
RadiationMonochromator: Flat collimating mirror; double crystal Si(111) monochromator; toroid mirror (vertical and horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 54042 / Num. obs: 52210 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 26.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 6.64 / Rsym value: 0.263 / % possible all: 92
Reflection
*PLUS
Num. measured all: 361546
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: Difference Fourier
Starting model: 1HP4

1hp4


Resolution: 2.1→43.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3178566.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 5254 10.1 %RANDOM
Rwork0.197 ---
all0.197 54042 --
obs0.197 52210 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.71 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å23.71 Å20 Å2
2--3.75 Å20 Å2
3----7.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 34 270 4168
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_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 800 9.8 %
Rwork0.225 7359 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAramPROTEIN.TOP
X-RAY DIFFRACTION2NEW_NGT_GOL.PARamNGT_GOL.TOP
X-RAY DIFFRACTION3SPECIAL_POSITION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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