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Yorodumi- PDB-4o47: Crystal structure of uncleaved guinea pig L-asparaginase type III -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o47 | ||||||
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Title | Crystal structure of uncleaved guinea pig L-asparaginase type III | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Cavia porcellus (domestic guinea pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Schalk, A.M. / Lavie, A. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structural and Kinetic Characterization of Guinea Pig l-Asparaginase Type III. Authors: Schalk, A.M. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o47.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o47.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 4o47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o47_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 4o47_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 4o47_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4o47_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/4o47 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o47 | HTTPS FTP |
-Related structure data
Related structure data | 4o48C 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: 34577.008 Da / Num. of mol.: 2 / Fragment: UNP residues 24-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: LOC100713636 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: H0VQC8, asparaginase #2: Chemical | #3: 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: 3.83 Å3/Da / Density % sol: 67.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES pH 6.0, 0.2 M ammonium sulfate, 13-15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2013 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 83861 / Num. obs: 83640 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.054 / Net I/σ(I): 14.75 |
Reflection shell | Resolution: 1.9→2.01 Å / Mean I/σ(I) obs: 2.59 / Num. unique all: 13338 / Rsym value: 0.496 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4GDV 4gdv Resolution: 1.9→28.73 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.114 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099 / 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: 43.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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