+Open data
-Basic information
Entry | Database: PDB / ID: 7uof | ||||||
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Title | Dihydroorotase from M. jannaschii | ||||||
Components | Dihydroorotase | ||||||
Keywords | HYDROLASE / DE NOVO PYRIMIDINE BIOSYNTHESIS / AMIDOHYDROLASE SUPERFAMILY / METALLOENZYME / ZINC BINDING / HISTIDINATE ANION | ||||||
Function / homology | Function and homology information dihydroorotase / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Vitali, J. / Nix, J.C. / Newman, H.E. / Colaneri, M.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2023 Title: Crystal structure of Methanococcus jannaschii dihydroorotase. Authors: Vitali, J. / Nix, J.C. / Newman, H.E. / Colaneri, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uof.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uof.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/7uof ftp://data.pdbj.org/pub/pdb/validation_reports/uo/7uof | HTTPS FTP |
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-Related structure data
Related structure data | 3mpgS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48226.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami2 (DE3) / References: UniProt: Q58885, dihydroorotase | ||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.7 % / Description: triangular prism |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 35% PEG400, 0.1 M Na Hepes pH 7.5, 0.1 M Zn acetate. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 18, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.9→48.18 Å / Num. obs: 57394 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.239 / Net I/σ(I): 9.7 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MPG Resolution: 1.9→48.18 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8194 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 33.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.18 Å
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Refine LS restraints |
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LS refinement shell |
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