+Open data
-Basic information
Entry | Database: PDB / ID: 5f52 | |||||||||
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Title | Erwinia chrysanthemi L-asparaginase + Aspartic acid | |||||||||
Components | L-asparaginaseAsparaginase | |||||||||
Keywords | HYDROLASE / L-asparaginase / Erwinia chrysanthemum / Aspartic acid | |||||||||
Function / homology | Function and homology information asparagine metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | |||||||||
Biological species | Dickeya chrysanthemi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Nguyen, H.A. / Lavie, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structural Insight into Substrate Selectivity of Erwinia chrysanthemi l-Asparaginase. Authors: Nguyen, H.A. / Su, Y. / Lavie, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f52.cif.gz | 279.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f52.ent.gz | 223.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/5f52 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/5f52 | HTTPS FTP |
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-Related structure data
Related structure data | 5hw0C 1o7jS 5f65 5f8d 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 4 - 327 / Label seq-ID: 5 - 328
NCS ensembles :
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-Components
#1: Protein | Mass: 35293.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Gene: ansB, asn / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P06608, asparaginase #2: Chemical | ChemComp-ASP / #3: Chemical | ChemComp-PEG / #4: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG MME 2000 / PH range: 7.4 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.629→88.037 Å / Num. obs: 151132 / % possible obs: 99.7 % / Redundancy: 7.25 % / Rsym value: 0.01 / Net I/σ(I): 15.65 |
Reflection shell | Resolution: 1.63→1.73 Å / Redundancy: 6.94 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 2.92 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O7J Resolution: 1.63→88.037 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1411 / FOM work R set: 0.8145 / SU B: 2.426 / SU ML: 0.075 / SU R Cruickshank DPI: 0.0878 / SU Rfree: 0.0874 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.05 Å2 / Biso mean: 17.698 Å2 / Biso min: 7.71 Å2
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Refinement step | Cycle: final / Resolution: 1.63→88.037 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.629→1.671 Å / Total num. of bins used: 20
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