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Yorodumi- PDB-1m04: Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m04 | ||||||
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Title | Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in complex with product (GlcNAc) | ||||||
Components | Beta-N-acetylhexosaminidaseHexosaminidase | ||||||
Keywords | HYDROLASE / substrate assisted catalysis / hexosaminidase / family 20 glycosidase | ||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / lysosome / carbohydrate metabolic process / membrane Similarity search - Function | ||||||
Biological species | Streptomyces plicatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Williams, S.J. / Mark, B.L. / Vocadlo, D.J. / James, M.N.G. / Withers, S.G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m04.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m04.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 1m04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m04 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m04 | HTTPS FTP |
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-Related structure data
Related structure data | 1m01C 1m03C 1hp4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 56125.793 Da / Num. of mol.: 1 / Mutation: D319N 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 |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 292 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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, NAG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 14, 2001 / Details: OSMIC optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. all: 65848 / Num. obs: 65848 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 19 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 19 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.256 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 1300022 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 98.5 % / Num. unique obs: 6556 / Rmerge(I) obs: 0.256 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1HP4 Resolution: 1.95→39.19 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.3872 Å2 / ksol: 0.377555 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→39.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 39.2 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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