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- PDB-1jak: Streptomyces plicatus beta-N-acetylhexosaminidase in Complex with... -

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Basic information

Entry
Database: PDB / ID: 1jak
TitleStreptomyces plicatus beta-N-acetylhexosaminidase in Complex with (2R,3R,4S,5R)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperidinium chloride (IFG)
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / glycoside hydrolase / family 20 / Beta-N-acetylhexosaminidase / substrate-assisted catalysis / alpha/beta barrel / isofagomine inhibitor complex
Function / homology
Function and homology information


Ca2+ activated K+ channels / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / calcium-activated potassium channel activity / beta-N-acetylhexosaminidase / ion channel inhibitor activity / cGMP effects / action potential / detection of calcium ion / potassium channel regulator activity ...Ca2+ activated K+ channels / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / calcium-activated potassium channel activity / beta-N-acetylhexosaminidase / ion channel inhibitor activity / cGMP effects / action potential / detection of calcium ion / potassium channel regulator activity / regulation of vasoconstriction / neuronal action potential / voltage-gated potassium channel complex / potassium ion transport / carbohydrate metabolic process / membrane / plasma membrane
Similarity search - Function
KCNMB2, ball/chain domain / KCNMB2, ball/chain domain superfamily / KCNMB2, ball and chain domain / Potassium channel, calcium-activated, BK, beta subunit / Calcium-activated potassium channel, beta subunit / 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 ...KCNMB2, ball/chain domain / KCNMB2, ball/chain domain superfamily / KCNMB2, ball and chain domain / Potassium channel, calcium-activated, BK, beta subunit / Calcium-activated potassium channel, beta subunit / 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-IFG / beta-N-acetylhexosaminidase / Calcium-activated potassium channel subunit beta-2
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsMark, B.L. / Vocadlo, D.J. / Zhao, D. / Knapp, S. / Withers, S.G. / James, M.N.
Citation
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.
#1: 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.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Aug 16, 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 30, 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)56,8109
Polymers56,1271
Non-polymers6838
Water9,530529
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.767, 132.767, 177.024
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-608-

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: p3AHEX-1.8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3)
References: UniProt: Q9Y691, UniProt: O85361*PLUS, beta-N-acetylhexosaminidase

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Non-polymers , 5 types, 537 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IFG / (2R,3R,4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE


Mass: 204.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2O4
#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.: 529 / 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: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulphate, Tri-sodium citrate, Sodium Chloride, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMtri-sodium citrate1droppH5.0
2300 mM1dropNaCl
310 mg/mlprotein1drop
42.1 Mammonium sulfate1reservoir
5100 mMtri-sodium 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 16, 2000
RadiationMonochromator: single crystal Si(331) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→44.1 Å / Num. all: 92286 / Num. obs: 92238 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 36.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 10.9 / Num. unique all: 4366 / % possible all: 95.7
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 92286 / Num. measured all: 1013193
Reflection shell
*PLUS
% possible obs: 95.7 % / Num. unique obs: 4366

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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: 1.75→44.1 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3274409.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 9315 10.1 %RANDOM
Rwork0.176 ---
all0.176 92238 --
obs0.176 92238 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å21.34 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.75→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 40 529 4433
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_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.372
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.204 1485 10 %
Rwork0.184 13301 -
obs-4366 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2IFG_GOL.PARAMIFG_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
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
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: 0.204 / % reflection Rfree: 10 % / Rfactor Rwork: 0.184

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