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- PDB-7r5q: Escherichia coli type II Asparaginase N24S mutant in complex with GLU -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r5q | ||||||
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Title | Escherichia coli type II Asparaginase N24S mutant in complex with GLU | ||||||
![]() | L-asparaginase 2 | ||||||
![]() | ANTITUMOR PROTEIN / 3.5.1.1 / Asparaginase / EcAII / hydrolase | ||||||
Function / homology | ![]() asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maggi, M. / Scotti, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Aspects of E. coli Type II Asparaginase in Complex with Its Secondary Product L-Glutamate. Authors: Maggi, M. / Scotti, C. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 664.2 KB | Display | ![]() |
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PDB format | ![]() | 561.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 69.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r57C ![]() 3ecaS C: citing same article ( S: Starting model for refinement |
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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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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GLU / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: HEPES pH 8.0, PEG 8000 7.5%, ETHYLENE GLYCOL 6% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 14, 2020 / Details: VERTICAL CRL | ||||||||||||||||||||||||||||||
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→47.81 Å / Num. obs: 161081 / % possible obs: 99.1 % / Redundancy: 3 % / Biso Wilson estimate: 32.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.046 / Rrim(I) all: 0.081 / Net I/σ(I): 7.8 / Num. measured all: 477220 / Scaling rejects: 1198 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ECA Resolution: 1.9→47.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.39 / Stereochemistry target values: ML
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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 max: 113.47 Å2 / Biso mean: 47.4111 Å2 / Biso min: 18.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→47.81 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 21.384 Å / Origin y: 31.5296 Å / Origin z: 29.0346 Å
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Refinement TLS group |
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