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Open data
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Basic information
Entry | Database: PDB / ID: 1ayy | ||||||
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Title | GLYCOSYLASPARAGINASE | ||||||
![]() | (GLYCOSYLASPARAGINASE) x 2 | ||||||
![]() | HYDROLASE / GLYCOAMIDASE | ||||||
Function / homology | ![]() N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / asparaginase activity / beta-aspartyl-peptidase activity / periplasmic space / lysosome / proteolysis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Van Roey, P. / Xuan, J. | ||||||
![]() | ![]() Title: Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum. Authors: Xuan, J. / Tarentino, A.L. / Grimwood, B.G. / Plummer Jr., T.H. / Cui, T. / Guan, C. / Van Roey, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.6 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 449.8 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16819.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #2: Protein | Mass: 15378.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #3: Water | ChemComp-HOH / | Compound details | THERE IS A SINGLE CHAIN PRECURSOR ACTIVATED BY PROTEOLYTI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 19% PEG3350 IN 100 MM TRIS.HCL PH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→20 Å / Num. obs: 22627 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3 / Rsym value: 0.17 / % possible all: 72.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HUMAN GLYCOSYLASPARAGINASE DIMER Resolution: 2.32→20 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 26.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.4 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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