[English] 日本語
Yorodumi- PDB-4osy: STRUCTURE of FULLY-CLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 4osy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE of FULLY-CLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN | |||||||||
Components | Isoaspartyl peptidase/L-asparaginase | |||||||||
Keywords | HYDROLASE / NTN ENZYME | |||||||||
Function / homology | Function and homology information beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / Phenylalanine metabolism / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / photoreceptor inner segment / proteolysis / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | |||||||||
Authors | Nomme, J. / Lavie, A. | |||||||||
Citation | Journal: Chem.Biol. / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4osy.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4osy.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 4osy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/4osy ftp://data.pdbj.org/pub/pdb/validation_reports/os/4osy | HTTPS FTP |
---|
-Related structure data
Related structure data | 4osxC 4gdt C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32232.639 Da / Num. of mol.: 2 / Fragment: L-asparaginase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASRGL1, ALP, CRASH / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 de3 c41 References: UniProt: Q7L266, beta-aspartyl-peptidase, asparaginase #2: Chemical | #3: Chemical | ChemComp-GLY / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7 Details: 2.2-2.5 M sodium Malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2012 | |||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL - LIQUED NITROGEN COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.91→51.74 Å / Num. obs: 45006 / % possible obs: 95.7 % / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 1.91→2.02 Å / % possible all: 81.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GDT 4gdt Resolution: 1.91→29.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.63 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 31.96 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→29.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|