+Open data
-Basic information
Entry | Database: PDB / ID: 7c8x | ||||||
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Title | Blasnase-T13A with L-asn | ||||||
Components | Asparaginase | ||||||
Keywords | HYDROLASE / substrate / complex / mutant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus sp. SUBG0010 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 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. #1: Journal: To Be Published Title: complex structure of BlAsnase with L-Asn Authors: Lu, F. / Ran, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c8x.cif.gz | 245.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c8x.ent.gz | 197.4 KB | Display | PDB format |
PDBx/mmJSON format | 7c8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/7c8x ftp://data.pdbj.org/pub/pdb/validation_reports/c8/7c8x | HTTPS FTP |
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-Related structure data
Related structure data | 7c8qC 7c91C 7cb4C 7cbrC 7cbuC 7cbwC 1o7jS 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 sp. SUBG0010 (bacteria) / Gene: DI291_14545 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2HLK7 #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-FMT / #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: 2.99 Å3/Da / Density % sol: 58.9 % |
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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 PILATUS3 S 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: 1.99→49.292 Å / Num. obs: 69445 / % possible obs: 99.7 % / Redundancy: 23.4 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.99→2.04 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4255 / CC1/2: 0.703 / Rpim(I) all: 0.323 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O7J Resolution: 1.994→49.292 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.169 / Average fsc free: 0.9343 / Average fsc work: 0.9409 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.111 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: 34.774 Å2
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Refinement step | Cycle: LAST / Resolution: 1.994→49.292 Å
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Refine LS restraints |
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LS refinement shell |
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