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- PDB-1hp5: STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE COMPLEXED WITH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hp5 | |||||||||
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Title | STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE COMPLEXED WITH INTERMEDIATE ANALOUGE NAG-THIAZOLINE | |||||||||
![]() | BETA-N-ACETYLHEXOSAMINIDASE | |||||||||
![]() | HYDROLASE / glycosyl hydrolase / streptomyces plicatus / hexosaminidase / family 20 / substrate assisted catalysis / TIM barrel | |||||||||
Function / homology | ![]() glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / lysosome / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Mark, B.L. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() Title: Cloning and expression of a Streptomyces plicatus chitinase (chitinase-63) in Escherichia coli Authors: Robbins, P.W. / Albright, C. / Benfield, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.4 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hp4SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 , 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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 277 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NGT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NGT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-NGT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.22 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2000 Details: Flat collimating mirror; double crystal Si(111) monochromator; toroid mirror (vertical and horizontal focusing) |
Radiation | Monochromator: 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 wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: Difference Fourier Starting model: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.71 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→43.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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