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Yorodumi- PDB-7e3u: Crystal structure of the Pseudomonas aeruginosa dihydropyrimidina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e3u | ||||||
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Title | Crystal structure of the Pseudomonas aeruginosa dihydropyrimidinase complexed with 5-AU | ||||||
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: 2.159 Å | ||||||
Authors | Yang, Y.C. / Luo, R.H. / Huang, Y.H. / Huang, C.Y. / Lin, E.S. | ||||||
Citation | Journal: Bioinorg Chem Appl / Year: 2022 Title: Molecular Insights into How the Dimetal Center in Dihydropyrimidinase Can Bind the Thymine Antagonist 5-Aminouracil: A Different Binding Mode from the Anticancer Drug 5-Fluorouracil. Authors: Lin, E.S. / Luo, R.H. / Yang, Y.C. / 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 | 7e3u.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e3u.ent.gz | 160.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e3u_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7e3u_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7e3u_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 7e3u_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e3u ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e3u | HTTPS FTP |
-Related structure data
Related structure data | 5e5cS S: Starting model for refinement |
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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: 52315.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: dht, PA0441 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9I676, dihydropyrimidinase #2: Chemical | ChemComp-WBU / | #3: Chemical | ChemComp-ZN / #4: 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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 16%PEG8000, 100mM HEPES pH7.5, 200mM Calcium Acetate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.159→30 Å / Num. obs: 64183 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.159→2.24 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 23.7 / Num. unique obs: 6340 / CC1/2: 0.866 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E5C Resolution: 2.159→28.012 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.35 Å2 / Biso mean: 36.4665 Å2 / Biso min: 14.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.159→28.012 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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