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- PDB-8bkf: Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bkf | ||||||
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Title | Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T (crystal M200T#o) | ||||||
![]() | (Isoaspartyl peptidase subunit ...) x 2 | ||||||
![]() | HYDROLASE / L-asparaginase / isoaspartylpeptidase / mutation / Ntn-hydrolase | ||||||
Function / homology | ![]() beta-aspartyl-peptidase / asparagine catabolic process via L-aspartate / asparaginase activity / beta-aspartyl-peptidase activity / protein autoprocessing / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sciuk, A. / Ruszkowski, M. / Jaskolski, M. / Loch, J.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The effects of nature-inspired amino acid substitutions on structural and biochemical properties of the E. coli L-asparaginase EcAIII. Authors: Janicki, M. / Sciuk, A. / Zielezinski, A. / Ruszkowski, M. / Ludwikow, A. / Karlowski, W.M. / Jaskolski, M. / Loch, J.I. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 42.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bi3C ![]() 8bp9C ![]() 8bqoC ![]() 8c0iC ![]() 8c23C ![]() 2zalS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Isoaspartyl peptidase subunit ... , 2 types, 4 molecules AAACCCBBBDDD
#1: Protein | Mass: 19013.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14398.055 Da / Num. of mol.: 2 / Mutation: M200T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 601 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-30% PEG4000,10-15% PEG400, 0,2 M magnesium chloride in 100mM Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→73.89 Å / Num. obs: 166404 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.075 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.22→1.24 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.696 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8052 / CC1/2: 0.596 / Rrim(I) all: 1.771 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZAL Resolution: 1.221→73.89 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.142 / SU ML: 0.022 / Cross valid method: NONE / ESU R: 0.032 / ESU R Free: 0.032 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.927 Å2
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Refinement step | Cycle: LAST / Resolution: 1.221→73.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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