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Yorodumi- PDB-7r57: Escherichia coli type II Asparaginase N24S mutant in its apo form -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r57 | ||||||
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Title | Escherichia coli type II Asparaginase N24S mutant in its apo form | ||||||
Components | L-asparaginase 2Asparaginase | ||||||
Keywords | ANTITUMOR PROTEIN / 3.5.1.1 / Asparaginase / EcAII / hydrolase | ||||||
Function / homology | Function and homology information asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Maggi, M. / Scotti, C. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Structural Aspects of E. coli Type II Asparaginase in Complex with Its Secondary Product L-Glutamate. Authors: Maggi, M. / Scotti, C. #1: Journal: Sci Rep / Year: 2017 Title: A protease-resistant Escherichia coli asparaginase with outstanding stability and enhanced anti-leukaemic activity in vitro. Authors: Maggi, M. / Mittelman, S.D. / Parmentier, J.H. / Colombo, G. / Meli, M. / Whitmire, J.M. / Merrell, D.S. / Whitelegge, J. / Scotti, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r57.cif.gz | 567.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r57.ent.gz | 379.3 KB | Display | PDB format |
PDBx/mmJSON format | 7r57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/7r57 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r57 | HTTPS FTP |
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-Related structure data
Related structure data | 7r5qC 3ecaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35428.660 Da / Num. of mol.: 4 / Mutation: N24S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ansB, b2957, JW2924 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ansA-/ansB- / References: UniProt: P00805, asparaginase #2: 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: 2.12 Å3/Da / Density % sol: 41.93 % / Description: Prism |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) 100 mM pH 8.0, PEG 8000 5%, ETHYLENE GLYCOL 4% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07252 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→48.2 Å / Num. obs: 261282 / % possible obs: 98.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.033 / Rrim(I) all: 0.058 / Net I/σ(I): 10.1 / Num. measured all: 724964 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ECA Resolution: 1.4→47.09 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2578 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→47.09 Å
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Refine LS restraints |
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LS refinement shell |
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