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Yorodumi- PDB-1u20: Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u20 | ||||||
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Title | Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29 | ||||||
Components | U8 snoRNA-binding protein X29 | ||||||
Keywords | HYDROLASE / modified Nudix hydrolase fold | ||||||
Function / homology | Function and homology information inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD+-cap (NAD+-forming) hydrolase activity / dITP diphosphatase activity / negative regulation of rRNA processing / NAD-cap decapping ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD+-cap (NAD+-forming) hydrolase activity / dITP diphosphatase activity / negative regulation of rRNA processing / NAD-cap decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / metalloexopeptidase activity / cobalt ion binding / snoRNA binding / mRNA catabolic process / manganese ion binding / nucleotide binding / mRNA binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Scarsdale, J.N. / Peculis, B.A. / Wright, H.T. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29 Authors: Scarsdale, J.N. / Peculis, B.A. / Wright, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u20.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u20.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1u20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u20 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u20 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24390.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6TEC1 #2: Chemical | #3: 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: 2.27 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.68 Details: 0.025 M HEPES, 3.75% PEG 6000, pH 7.68, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 20, 2004 / Details: Osmic Confocal optics |
Radiation | Monochromator: Osmic confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26.8 Å / Num. all: 27307 / Num. obs: 27224 / Redundancy: 6.8 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.355 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→26.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.772 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.203 / 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: 38.719 Å2
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Refine analyze | Luzzati coordinate error obs: 0.287 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→26.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 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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