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Yorodumi- PDB-3ehw: Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: vis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ehw | ||||||
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Title | Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site | ||||||
Components | dUTP pyrophosphatase | ||||||
Keywords | HYDROLASE / jelly-roll / full-length C-terminal arm / enzyme-ligand complex | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / dTMP biosynthetic process / DNA replication / magnesium ion binding ...dUTP catabolic process / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / dTMP biosynthetic process / DNA replication / magnesium ion binding / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Takacs, E. / Barabas, O. / Vertessy, B.G. | ||||||
Citation | Journal: To be Published Title: Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site Authors: Takacs, E. / Barabas, O. / Vertessy, B.G. #1: Journal: Structure / Year: 1996 Title: Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Authors: Mol, C.D. / Harris, J.M. / McIntosh, E.M. / Tainer, J.A. #2: Journal: FEBS Lett. / Year: 2007 Title: Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase. Authors: Varga, B. / Barabas, O. / Kovari, J. / Toth, J. / Hunyadi-Gulyas, E. / Klement, E. / Medzihradszky, K.F. / Tolgyesi, F. / Fidy, J. / 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 | 3ehw.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ehw.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ehw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ehw_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 3ehw_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3ehw_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 3ehw_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/3ehw ftp://data.pdbj.org/pub/pdb/validation_reports/eh/3ehw | 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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Unit cell |
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-Components
#1: Protein | Mass: 17771.068 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6FHN1, UniProt: P33316*PLUS, dUTP diphosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-DUP / #4: 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: 1.89 Å3/Da / Density % sol: 34.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES buffer, containing 20% PEG 3350 and 200 mM sodium chloride, pH 7.5, 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: X13 / Wavelength: 0.8031 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2004 / Details: BENT, VERTICALLY FOCUSING MIRROR |
Radiation | Monochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8031 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 70417 / Num. obs: 70417 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.17 % / Biso Wilson estimate: 26.26 Å2 / Rsym value: 0.071 / Net I/σ(I): 10.15 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.13 % / Mean I/σ(I) obs: 2.24 / Num. unique all: 10689 / Rsym value: 0.475 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q5U Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.299 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.129 / 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: 23.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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