+Open data
-Basic information
Entry | Database: PDB / ID: 1dup | ||||||
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Title | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE (D-UTPASE) | ||||||
Components | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE | ||||||
Keywords | HYDROLASE / NUCLEOTIDE METABOLISM | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Dauter, Z. / Wilson, K.S. / Larsson, G. / Nyman, P.O. / Cedergren, E. | ||||||
Citation | Journal: Nature / Year: 1992 Title: Crystal structure of a dUTPase. Authors: Cedergren-Zeppezauer, E.S. / Larsson, G. / Nyman, P.O. / Dauter, Z. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dup.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dup.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dup_validation.pdf.gz | 414.3 KB | Display | wwPDB validaton report |
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Full document | 1dup_full_validation.pdf.gz | 418.1 KB | Display | |
Data in XML | 1dup_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1dup_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1dup ftp://data.pdbj.org/pub/pdb/validation_reports/du/1dup | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 STRUCTURE IS BUILT-UP OF TIGHT TRIMERS AROUND THE CRYSTALLOGRAPHIC THREE-FOLD AXIS. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 136 1 .. 136 M2 A 1 .. A 136 1 .. 136 THESE TRANSFORMATIONS WILL YIELD THE COORDINATES FOR THE TWO OTHER SUBUNITS OF THE TRIMER. |
-Components
#1: Protein | Mass: 16302.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: S2 / References: UniProt: P06968, dUTP diphosphatase |
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#2: Water | ChemComp-HOH / |
Compound details | SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS ...SECONDARY STRUCTURE BOUNDARIES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.36 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.2 / Method: other | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 13640 / % possible obs: 96 % / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Resolution: 1.9→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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