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Yorodumi- PDB-5dne: Crystal structure of the Asn-bound guinea pig L-asparaginase 1 ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dne | ||||||
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Title | Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant K188M | ||||||
Components | L-asparaginaseAsparaginase | ||||||
Keywords | HYDROLASE / asparaginase | ||||||
Function / homology | Function and homology information aspartate family amino acid metabolic process / asparaginase / asparaginase activity Similarity search - Function | ||||||
Biological species | Cavia porcellus (domestic guinea pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Schalk, A.M. / Lavie, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Experimental Data in Support of a Direct Displacement Mechanism for Type I/II l-Asparaginases. Authors: Schalk, A.M. / Antansijevic, A. / Caffrey, 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 | 5dne.cif.gz | 296.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dne.ent.gz | 231.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/5dne ftp://data.pdbj.org/pub/pdb/validation_reports/dn/5dne | HTTPS FTP |
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-Related structure data
Related structure data | 5dncC 5dndC 4r8lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 63386.758 Da / Num. of mol.: 4 / Mutation: K188M Source method: isolated from a genetically manipulated source Details: The first 23 residues are from the tag hexahistidine tag and TEV protease cleavage site. They were not removed during purification but are not seen in the structure. The C-terminus of the ...Details: The first 23 residues are from the tag hexahistidine tag and TEV protease cleavage site. They were not removed during purification but are not seen in the structure. The C-terminus of the protein was cleaved in the drop and is not seen in the structure despite being present throughout the entirety of the purification. Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: ASPG / Plasmid: pET14b Details (production host): hexahistidine tag and TEV protease site Production host: Escherichia coli (E. coli) / References: UniProt: H0W0T5 #2: Chemical | ChemComp-ASN / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.49 Å3/Da / Density % sol: 17.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 12-15% PEG 4000 |
-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 23, 2015 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→30 Å / Num. obs: 57320 / % possible obs: 95.5 % / Redundancy: 3.2 % / Rsym value: 0.12 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.39→2.53 Å / Redundancy: 3.1 % / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4r8l Resolution: 2.39→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.839 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.537 / ESU R Free: 0.268 / 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: 40.279 Å2
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Refinement step | Cycle: 1 / Resolution: 2.39→30 Å
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Refine LS restraints |
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