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- PDB-1hp4: CRYSTAL STRUCTURE OF STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE -

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Basic information

Entry
Database: PDB / ID: 1hp4
TitleCRYSTAL STRUCTURE OF STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE
ComponentsBETA-N-ACETYLHEXOSAMINIDASE
KeywordsHYDROLASE / glycosyl hydrolase / hexosaminidase / Streptomyces plicatus / family 20 / TIM barrel
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / carbohydrate metabolic process
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 / SYNCHROTRON / MAD / Resolution: 2.2 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: Gene / Year: 1992
Title: Cloning and High-level Expression of Chitinase-encoding Gene of Streptomyces plicatus
Authors: Robbins, P.W. / Overbye, K. / Albright, C. / Benfield, B. / Pero, J.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 2001
Title: Biochemical and Structural Assessment of the 1-N-Azasugar GalNAc-isofagomine as a Potent Family 20 beta -N-Acetylhexosaminidase Inhibitor.
Authors: Mark, B.L. / Vocadlo, D.J. / Zhao, D. / Knapp, S. / Withers, S.G. / James, M.N.
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 2.0Oct 16, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)56,6419
Polymers56,1271
Non-polymers5148
Water6,882382
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)113,28218
Polymers112,2542
Non-polymers1,02816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6030 Å2
ΔGint-138 kcal/mol
Surface area32360 Å2
MethodPISA, PQS
3
A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules

A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,28218
Polymers112,2542
Non-polymers1,02816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area3630 Å2
ΔGint-88 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.100, 133.100, 176.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulphate, tri-sodium citrate, 20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2 Mammonium sulfate1reservoir
2100 mMtrisodium citrate1reservoirpH6.0
320-25 %glycerol1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9797, 0.9795, 0.9496
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 1999
RadiationMonochromator: Triangle Ge(111), Conical Si/Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97951
30.94961
ReflectionResolution: 2.2→40 Å / Num. all: 47477 / Num. obs: 47413 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 56.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 21.6 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 416806
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 99.3 % / Num. unique obs: 3854

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→32.19 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3258301.65 / 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
Rfree0.209 4783 10.1 %RANDOM
Rwork0.181 ---
all0.181 47455 --
obs0.181 47413 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.07 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å21.69 Å20 Å2
2--0.75 Å20 Å2
3----1.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 27 382 4273
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_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 739 9.6 %
Rwork0.175 6987 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAramPROTEIN.TOP
X-RAY DIFFRACTION2GOL_XPLOR_PAR.TXTGOL_XPLOR_TOP.TXT
X-RAY DIFFRACTION3SPECIAL_POSITION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAmION.TOP
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.214 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.175

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