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Yorodumi- PDB-6l0i: Crystal structure of dihydroorotase in complex with malate at pH6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l0i | ||||||
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Title | Crystal structure of dihydroorotase in complex with malate at pH6.5 from Saccharomyces cerevisiae | ||||||
Components | Dihydroorotase | ||||||
Keywords | HYDROLASE / Dihydropyrimidinase Dihydroorotase metalloenzyme | ||||||
Function / homology | Function and homology information dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Guan, H.H. / Huang, Y.H. / Huang, C.Y. / Chen, C.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Structural basis for the interaction modes of dihydroorotase with the anticancer drugs 5-fluorouracil and 5-aminouracil. Authors: Guan, H.H. / Huang, Y.H. / Lin, E.S. / Chen, C.J. / 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 | 6l0i.cif.gz | 308.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l0i.ent.gz | 248.4 KB | Display | PDB format |
PDBx/mmJSON format | 6l0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/6l0i ftp://data.pdbj.org/pub/pdb/validation_reports/l0/6l0i | HTTPS FTP |
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-Related structure data
Related structure data | 6l0bC 6l0fC 6l0gC 6l0hC 6l0kC 6l0aS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41478.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: URA4, YLR420W, L9931.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20051, dihydroorotase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-LMR / ( #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: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM imidazole malate pH 6.5, 18% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.215 Å / Num. obs: 76236 / % possible obs: 97.76 % / Redundancy: 3.8 % / CC1/2: 0.935 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Num. unique obs: 6417 / CC1/2: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L0A Resolution: 2.2→37.215 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.74 Å2 / Biso mean: 25.5405 Å2 / Biso min: 3.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→37.215 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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