+Open data
-Basic information
Entry | Database: PDB / ID: 3ecy | ||||||
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Title | Crystal structural analysis of Drosophila melanogaster dUTPase | ||||||
Components | CG4584-PA, isoform A (BcDNA.LD08534) | ||||||
Keywords | HYDROLASE / jelly-roll / dimeric assembly | ||||||
Function / homology | Function and homology information dUTP metabolic process / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Takacs, E. / Barabas, O. / Vertessy, B.G. | ||||||
Citation | Journal: Febs Lett. / Year: 2009 Title: Molecular shape and prominent role of beta-strand swapping in organization of dUTPase oligomers. Authors: Takacs, E. / Barabas, O. / Petoukhov, M.V. / Svergun, D.I. / Vertessy, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ecy.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ecy.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ecy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ecy_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 3ecy_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 3ecy_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3ecy_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/3ecy ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ecy | HTTPS FTP |
-Related structure data
Related structure data | 1q5uS 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
#1: Protein | Mass: 17353.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dUTPase, BcDNA.LD08534, CG4584, Dmel_CG4584 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9V3I1, dUTP diphosphatase #2: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 50 mM sodium succinate buffer, 200 mM sodium chloride, 30-35% methyl-pentane diol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8457 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8457 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→20 Å / Num. all: 28229 / Num. obs: 28229 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.45 % / Biso Wilson estimate: 41.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.95 |
Reflection shell | Resolution: 1.78→1.89 Å / Redundancy: 6.84 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4348 / Rsym value: 0.74 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q5U Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.337 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.122 / 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: 41.067 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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