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- PDB-5dnd: Crystal structure of the Asn-bound guinea pig L-asparaginase 1 ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dnd | ||||||
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Title | Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A | ||||||
![]() | L-asparaginase | ||||||
![]() | HYDROLASE / asparaginase | ||||||
Function / homology | ![]() aspartate family amino acid metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schalk, A.M. / Lavie, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298 KB | Display | ![]() |
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PDB format | ![]() | 233 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.2 KB | Display | ![]() |
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Full document | ![]() | 514 KB | Display | |
Data in XML | ![]() | 52.9 KB | Display | |
Data in CIF | ![]() | 74.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dncC ![]() 5dneC ![]() 4r8lS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _
NCS ensembles :
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Details | Tetramer by Gel filtration |
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Components
#1: Protein | Mass: 63354.719 Da / Num. of mol.: 4 / Mutation: T116A 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.) ![]() Details (production host): hexahistidine tag and TEV protease site Production host: ![]() ![]() #2: Chemical | ChemComp-ASN / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.49 Å3/Da / Density % sol: 17.3 % |
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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: ![]() ![]() ![]() |
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: 2.29→30 Å / Num. obs: 66847 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rsym value: 0.12 / Net I/σ(I): 13.38 |
Reflection shell | Resolution: 2.29→2.43 Å / Redundancy: 5.1 % / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4r8l Resolution: 2.29→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.12 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.241 / 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: 37.695 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→30 Å
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Refine LS restraints |
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