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Yorodumi- PDB-5e5c: Crystal structure of dihydropyrimidinase from Pseudomonas aerugin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e5c | ||||||
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Title | Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 | ||||||
Components | D-hydantoinase/dihydropyrimidinase | ||||||
Keywords | HYDROLASE / dihydropyrimidinase | ||||||
Function / homology | Function and homology information dihydropyrimidinase / dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Huang, C.C. / Huang, Y.H. / Hsieh, Y.C. / Tzeng, C.T. / Chen, C.J. / Huang, C.Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1: Insights into the molecular basis of formation of a dimer Authors: Tzeng, C.T. / Huang, Y.H. / Huang, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e5c.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5c.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 5e5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5c ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5c | HTTPS FTP |
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-Related structure data
Related structure data | 2ftwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53144.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dht, PA0441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I676, dihydropyrimidinase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: 10% PEG8000, 100mM HEPES sodium salt, 200mM Calcium Acetate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→97.11 Å / Num. all: 68937 / Num. obs: 68799 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.21 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.976 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FTW Resolution: 2.1→97.11 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.515 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.554 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→97.11 Å
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Refine LS restraints |
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