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Yorodumi- PDB-1seh: Crystal structure of E. coli dUTPase complexed with the product dUMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1seh | ||||||
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Title | Crystal structure of E. coli dUTPase complexed with the product dUMP | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / enzyme-ligand complex / jelly roll | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / protein homotrimerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Barabas, O. / Kovari, J. / Pongracz, V. / Wilmanns, M. / Vertessy, B.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase Authors: Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Atomic resolution structure of Escherichia coli dUTPase determined ab initio Authors: Gonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1seh.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1seh.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1seh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1seh_validation.pdf.gz | 813.5 KB | Display | wwPDB validaton report |
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Full document | 1seh_full_validation.pdf.gz | 813.6 KB | Display | |
Data in XML | 1seh_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1seh_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1seh ftp://data.pdbj.org/pub/pdb/validation_reports/se/1seh | HTTPS FTP |
-Related structure data
Related structure data | 1rn8C 1rnjC 1sylC 1euwS 1ro1 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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 hexamer generated from the monomer in the asymmetric unit by the operations: 1-y,1+x-y,z and -x+y,1-x,z. |
-Components
#1: Protein | Mass: 16302.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DUT / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06968, dUTP diphosphatase |
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#2: Chemical | ChemComp-UMP / |
#3: Chemical | ChemComp-TRS / |
#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: 2.26 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 3350, SODIUM ACETATE, TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.804 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2003 |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.804 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→20 Å / Num. obs: 29251 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 31.8 % / Rsym value: 0.083 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.47→1.6 Å / Redundancy: 20.09 % / Mean I/σ(I) obs: 4.86 / Num. unique all: 6421 / Rsym value: 0.73 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EUW Resolution: 1.47→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.057 / SU ML: 0.04 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Although the Rsym is quite high in the last shell, this shell still contains a significant amount of good and useful data (I/sigmaI is 4.86).
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.137 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Total num. of bins used: 20
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