+Open data
-Basic information
Entry | Database: PDB / ID: 8h4g | ||||||
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Title | Blasnase-T13A/M57N | ||||||
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: 1.81 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 | 8h4g.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h4g.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 8h4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/8h4g ftp://data.pdbj.org/pub/pdb/validation_reports/h4/8h4g | HTTPS FTP |
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-Related structure data
Related structure data | 8h44C 8h45C 8h46C 8h47C 8h48C 8h49C 8h4aC 8h4bC 8h4cC 8h4dC 8h4eC 8h4fC 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: 36361.109 Da / Num. of mol.: 2 / Mutation: T13A, M57N 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 | #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: 3.41 Å3/Da / Density % sol: 63.98 % |
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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: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→19.95 Å / Num. obs: 92541 / % possible obs: 99.9 % / Redundancy: 25.8 % / CC1/2: 0.998 / Rpim(I) all: 0.033 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.81→1.84 Å / Num. unique obs: 4498 / CC1/2: 0.602 / Rpim(I) all: 0.642 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C8X Resolution: 1.81→19.95 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 38.31 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→19.95 Å
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Refine LS restraints |
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