+Open data
-Basic information
Entry | Database: PDB / ID: 8h49 | ||||||
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Title | Blasnase-M57P | ||||||
Components | L-asparaginaseAsparaginase | ||||||
Keywords | HYDROLASE / Mutant | ||||||
Function / homology | Function and homology information asparagine metabolic process / asparaginase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus paralicheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lu, F. / Wang, W. / Chi, H. / Ran, T. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure-based rational design of Bacillus licheniformis L-asparaginase with low/no D-asparaginase activity for a safer enzyme Authors: Lu, F. / Wang, W. / Chi, H. / Ran, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h49.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h49.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/8h49 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/8h49 | HTTPS FTP |
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-Related structure data
Related structure data | 8h44C 8h45C 8h46C 8h47C 8h48C 8h4aC 8h4bC 8h4cC 8h4dC 8h4eC 8h4fC 8h4gC 7c8xS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36236.000 Da / Num. of mol.: 2 / Mutation: M57P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus paralicheniformis (bacteria) / Gene: B4121_3474 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I7U6Y2 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.36 Å3/Da / Density % sol: 63.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: sodium formate |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.67 Å / Num. obs: 66776 / % possible obs: 98.9 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 4403 / CC1/2: 0.732 / Rpim(I) all: 0.425 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C8X Resolution: 2→41.39 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 47.19 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.39 Å
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Refine LS restraints |
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