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Yorodumi- PDB-4o0d: Crystal structure of the human L-asparaginase protein T168S mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o0d | ||||||
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Title | Crystal structure of the human L-asparaginase protein T168S mutant | ||||||
Components | Isoaspartyl peptidase/L-asparaginase | ||||||
Keywords | HYDROLASE / NTN ENZYME / HOMODIMER / asparaginase | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Nomme, J. / Lavie, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Elucidation of the Specific Function of the Conserved Threonine Triad Responsible for Human l-Asparaginase Autocleavage and Substrate Hydrolysis. Authors: Nomme, J. / Su, Y. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o0d.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o0d.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 4o0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o0d_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 4o0d_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 4o0d_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 4o0d_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/4o0d ftp://data.pdbj.org/pub/pdb/validation_reports/o0/4o0d | HTTPS FTP |
-Related structure data
Related structure data | 4o0cC 4o0eC 4o0fC 4o0gC 4o0hC 4gdv 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32218.615 Da / Num. of mol.: 2 / Mutation: T168S 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 / | |
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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: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2-2.5 M sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||
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→30 Å / Num. all: 36456 / Num. obs: 36456 / % possible obs: 82.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.89 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.75 | |||||||||||||||
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.18 / % possible all: 71.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4GDV 4gdv Resolution: 1.95→29.27 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.595 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.039 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.645 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.002 Å / Total num. of bins used: 20
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