+Open data
-Basic information
Entry | Database: PDB / ID: 1q5h | ||||||
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Title | Human dUTP Pyrophosphatase complex with dUDP | ||||||
Components | dUTP pyrophosphatase | ||||||
Keywords | HYDROLASE / DNA repair / enzyme-DNA interactions | ||||||
Function / homology | Function and homology information pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / signaling receptor inhibitor activity / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / signaling receptor inhibitor activity / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / response to organic cyclic compound / DNA replication / magnesium ion binding / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / nucleus / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mol, C.D. / Harris, J.M. / McIntosh, E.M. / Tainer, J.A. | ||||||
Citation | 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q5h.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q5h.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1q5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/1q5h ftp://data.pdbj.org/pub/pdb/validation_reports/q5/1q5h | HTTPS FTP |
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-Related structure data
Related structure data | 1q5uC 1dupS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | the crystallographic asymmetric unit contains the biologically relevant trimer. |
-Components
#1: Protein | Mass: 16244.277 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEM409 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33316 #2: Chemical | ChemComp-MG / | #3: Chemical | #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: 2.21 Å3/Da / Density % sol: 44.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 1996 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 28406 / Num. obs: 28406 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.62 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2412 / Rsym value: 0.323 / % possible all: 82 |
Reflection | *PLUS Num. measured all: 102902 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 82 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DUP Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.721 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 13.189 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.052 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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Refinement | *PLUS Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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