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Yorodumi- PDB-1jak: Streptomyces plicatus beta-N-acetylhexosaminidase in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jak | |||||||||
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Title | Streptomyces plicatus beta-N-acetylhexosaminidase in Complex with (2R,3R,4S,5R)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperidinium chloride (IFG) | |||||||||
Components | Beta-N-acetylhexosaminidase | |||||||||
Keywords | HYDROLASE / 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 / calcium-activated potassium channel activity / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / ion channel inhibitor activity / cGMP effects / action potential / neuronal action potential ...Ca2+ activated K+ channels / calcium-activated potassium channel activity / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / ion channel inhibitor activity / cGMP effects / action potential / neuronal action potential / detection of calcium ion / regulation of vasoconstriction / potassium channel regulator activity / voltage-gated potassium channel complex / beta-N-acetylglucosaminidase activity / potassium ion transport / carbohydrate metabolic process / lysosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Streptomyces plicatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | |||||||||
Authors | Mark, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jak.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jak.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1jak ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1jak | HTTPS FTP |
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-Related structure data
Related structure data | 1hp4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-IFG / ( | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.32 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 2000 |
Radiation | Monochromator: single crystal Si(331) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1 Å2 / ksol: 0.391 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→44.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor Rfree: 0.204 / % reflection Rfree: 10 % / Rfactor Rwork: 0.184 |