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Yorodumi- PDB-8wq9: Crystal structure of dihydropyrimidinase complexed with gamma-ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wq9 | ||||||
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Title | Crystal structure of dihydropyrimidinase complexed with gamma-aminobutyric acid | ||||||
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 PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Huang, Y.H. / Huang, C.Y. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: The complexed crystal structure of dihydropyrimidinase reveals a potential interactive link with the neurotransmitter gamma-aminobutyric acid (GABA). Authors: 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 | 8wq9.cif.gz | 211 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wq9.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 8wq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wq9_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 8wq9_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8wq9_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 8wq9_validation.cif.gz | 62.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/8wq9 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/8wq9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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 PAO1 (bacteria) / Strain: PAO1 / Gene: dht, PA0441 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I676, dihydropyrimidinase #2: Chemical | ChemComp-ABU / #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: 2.6 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18%PEG8000, 100mM Tris-HCl pH7.0, 200mM Calcium Chloride |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. obs: 75195 / % possible obs: 95.4 % / Redundancy: 3.4 % / CC1/2: 0.976 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 7479 / CC1/2: 0.921 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→27.74 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.48 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→27.74 Å
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Refine LS restraints |
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LS refinement shell |
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