+Open data
-Basic information
Entry | Database: PDB / ID: 7cbu | ||||||
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Title | Blasnase-T13A with L-Asp | ||||||
Components | L-asparaginaseAsparaginase | ||||||
Keywords | HYDROLASE / substrate / complex / mutant | ||||||
Function / homology | Function and homology information cellular anatomical entity / 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: 2.25 Å | ||||||
Authors | Lu, F. / Ran, T. / Jiao, L. / Wang, W. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2021 Title: Structures of l-asparaginase from Bacillus licheniformis Reveal an Essential Residue for its Substrate Stereoselectivity. Authors: Ran, T. / Jiao, L. / Wang, W. / Chen, J. / Chi, H. / Lu, Z. / Zhang, C. / Xu, D. / Lu, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cbu.cif.gz | 239.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cbu.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 7cbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/7cbu ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cbu | HTTPS FTP |
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-Related structure data
Related structure data | 7c8qC 7c8xC 7c91SC 7cb4C 7cbrC 7cbwC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 41407.691 Da / Num. of mol.: 2 / Mutation: T13A 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: A0A1Q8GMZ7, UniProt: A0A6I7U6Y2*PLUS #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.03 Å3/Da / Density % sol: 59.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→19.925 Å / Num. obs: 49335 / % possible obs: 99.9 % / Redundancy: 24.6 % / CC1/2: 0.999 / Rpim(I) all: 0.041 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.25→2.32 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4447 / CC1/2: 0.724 / Rpim(I) all: 0.408 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C91 Resolution: 2.25→19.925 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.183 / Average fsc free: 0.9078 / Average fsc work: 0.9155 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.165 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: 43.808 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→19.925 Å
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Refine LS restraints |
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LS refinement shell |
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