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- PDB-4osx: STRUCTURE of UNCLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN -
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Open data
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Basic information
Entry | Database: PDB / ID: 4osx | |||||||||
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Title | STRUCTURE of UNCLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN | |||||||||
![]() | Isoaspartyl peptidase/L-asparaginase | |||||||||
![]() | HYDROLASE / NTN ENZYME | |||||||||
Function / homology | ![]() beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / Phenylalanine metabolism / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / photoreceptor inner segment / proteolysis / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nomme, J. / Lavie, A. | |||||||||
![]() | ![]() Title: Free Glycine Accelerates the Autoproteolytic Activation of Human Asparaginase. Authors: Su, Y. / Karamitros, C.S. / Nomme, J. / Mcsorley, T. / Konrad, M. / Lavie, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.9 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.3 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4osyC ![]() 4gdt C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32232.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7L266, beta-aspartyl-peptidase, asparaginase #2: Chemical | #3: Chemical | ChemComp-GLY / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 2.2 M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2012 | |||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL - LIQUID NITROGEN COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.95→51.91 Å / Num. obs: 43500 / % possible obs: 94.7 % / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 1.95→2 Å / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4GDT ![]() 4gdt Resolution: 1.95→29.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.502 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.39 Å
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Refine LS restraints |
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