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Yorodumi- PDB-1ui0: Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermoph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ui0 | |||||||||
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Title | Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8 | |||||||||
Components | Uracil-DNA Glycosylase | |||||||||
Keywords | HYDROLASE / Base Excision Repair / Uracil-DNA Glycosylase / Iron/Sulfer Cluster / Thermophile / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | |||||||||
Function / homology | Function and homology information uracil-DNA glycosylase / uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Hoseki, J. / Okamoto, A. / Masui, R. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of a Family 4 Uracil-DNA Glycosylase from Thermus thermophilus HB8 Authors: Hoseki, J. / Okamoto, A. / Masui, R. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ui0.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ui0.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ui0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/1ui0 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/1ui0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22997.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: tthung / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q7WYV4, UniProt: Q5SKC5*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-SF4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.73 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2-1.5M ammonium sulfate, 75mM Tris, 25% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.98 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 23, 2002 |
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.2 Å / Num. obs: 35830 / % possible obs: 99.9 % / Biso Wilson estimate: 10.1 Å2 |
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 163400 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.133 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Selenomethionyl uracil-DNA glycosylase from Thermus thermophilus HB8 Resolution: 1.5→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 87702.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.448 Å2 / ksol: 0.481203 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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