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Yorodumi- PDB-2ftw: Crystal structure of dihydropyrimidinase from dictyostelium discoideum -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ftw | ||||||
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Title | Crystal structure of dihydropyrimidinase from dictyostelium discoideum | ||||||
Components | dihydropyrimidine amidohydrolase | ||||||
Keywords | HYDROLASE / (BETA-ALPHA)8-BARREL / BETA-SANDWICH | ||||||
Function / homology | Function and homology information Pyrimidine catabolism / dihydropyrimidinase / pyrimidine nucleobase catabolic process / dihydropyrimidinase activity / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Lohkamp, B. / Dobritzsch, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship between Cyclic Amidohydrolases and Explain Their Substrate Specificity. Authors: Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ftw.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ftw.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ftw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ftw ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ftw | HTTPS FTP |
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-Related structure data
Related structure data | 2ftyC 2fvkC 2fvmC 1kcxS 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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: 1-x, -y, z and 1-x, y, -z and x, -y, -z. |
-Components
#1: Protein | Mass: 58342.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: pyd2 / Plasmid: p343 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q86LT2, UniProt: Q55DL0*PLUS, dihydropyrimidinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-MLI / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% PEG 1500, 0.1M MMT buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.459 Å / Num. obs: 30568 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.05→2.16 Å / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 0.9 / Num. measured all: 12225 / Num. unique all: 30568 / Num. unique obs: 4408 / Rsym value: 0.662 / % possible all: 94.4 |
-Phasing
Phasing MR | Rfactor: 0.432 / Cor.coef. Fo:Fc: 0.55
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KCX Resolution: 2.05→25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.544 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.202 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.157 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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