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Yorodumi- PDB-8c8i: Human dUTPase in complex with a potent proteinaceous inhibitor (Stl) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c8i | ||||||
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Title | Human dUTPase in complex with a potent proteinaceous inhibitor (Stl) | ||||||
Components |
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Keywords | HYDROLASE / Inhibitor / Complex / dUTPase | ||||||
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 / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Kohegyi, B.K. / Nyiri, K. / Vertessy, B.G. | ||||||
Funding support | Hungary, 1items
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Citation | Journal: To Be Published Title: Human dUTPase in complex with a potent proteinaceous inhibitor (Stl) Authors: Kohegyi, B.K. / Nyiri, K. / 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 | 8c8i.cif.gz | 323 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c8i.ent.gz | 260.1 KB | Display | PDB format |
PDBx/mmJSON format | 8c8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c8i_validation.pdf.gz | 680.1 KB | Display | wwPDB validaton report |
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Full document | 8c8i_full_validation.pdf.gz | 684.5 KB | Display | |
Data in XML | 8c8i_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 8c8i_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/8c8i ftp://data.pdbj.org/pub/pdb/validation_reports/c8/8c8i | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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 ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 14178.108 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Production host: Escherichia coli (E. coli) / References: UniProt: P33316, dUTP diphosphatase #2: Protein | Mass: 17209.420 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8 #3: Chemical | ChemComp-MG / | Has ligand of interest | Y | |
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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: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Ammonium sulfate, Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021 |
Radiation | Monochromator: Double Crystal Si111 with LN2 closed loop cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→71.1 Å / Num. obs: 15601 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 73.54 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.2→3.37 Å / Rmerge(I) obs: 1.077 / Num. unique obs: 2232 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→52.69 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→52.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.1913 Å / Origin y: 8.7573 Å / Origin z: 11.2703 Å
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Refinement TLS group | Selection details: all |