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Yorodumi- PDB-2hqu: Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hqu | ||||||
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Title | Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / jelly-roll / protein-substrate analogue ligand complex | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / 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 ...dUTP catabolic process / dUMP biosynthetic process / 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: 2.2 Å | ||||||
Authors | Barabas, O. / Varga, B. / Vertessy, B.G. | ||||||
Citation | 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. #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. | ||||||
History |
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Remark 999 | SEQUENCE The protein used in this study is an isoform SWS P33316-2 of the protein in the database reference |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hqu.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hqu.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hqu_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2hqu_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2hqu_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2hqu_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/2hqu ftp://data.pdbj.org/pub/pdb/validation_reports/hq/2hqu | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 24 - 146 / Label seq-ID: 24 - 146
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Details | the biological assembly is the trimer found in the asymmetric unit |
-Components
#1: Protein | Mass: 17771.068 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUTN / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P33316, dUTP diphosphatase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 1.68 Å3/Da / Density % sol: 26.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18-20% PEG 3350, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Temp details: 293 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8124 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Details: mirror |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8124 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 21420 / Num. obs: 21420 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 1.2 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.116 / Net I/σ(I): 9.21 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 3.69 / Num. unique all: 2736 / Rsym value: 0.33 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q5U truncated at residue 146 Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.788 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.241 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.252 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 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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