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Yorodumi- PDB-1xe0: The structure and function of Xenopus NO38-core, a histone bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xe0 | ||||||
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Title | The structure and function of Xenopus NO38-core, a histone binding chaperone in the nucleolus | ||||||
Components | Nucleophosmin | ||||||
Keywords | CHAPERONE / NO38 / Drosophila Nucleoplasmin-Like Protein (dNLP) / Nucleoplasmin (Np) / histone binding | ||||||
Function / homology | Function and homology information regulation of endoribonuclease activity / regulation of endodeoxyribonuclease activity / regulation of centrosome duplication / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / histone binding / chromatin remodeling / ribonucleoprotein complex ...regulation of endoribonuclease activity / regulation of endodeoxyribonuclease activity / regulation of centrosome duplication / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / histone binding / chromatin remodeling / ribonucleoprotein complex / DNA repair / chromatin binding / centrosome / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Namboodiri, V.M. / Akey, I.V. / Schmidt-Zachmann, M.S. / Head, J.F. / Akey, C.W. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The Structure and Function of Xenopus NO38-Core, a Histone Chaperone in the Nucleolus. Authors: Namboodiri, V.M. / Akey, I.V. / Schmidt-Zachmann, M.S. / Head, J.F. / Akey, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xe0.cif.gz | 208.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xe0.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 1xe0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xe0_validation.pdf.gz | 506.1 KB | Display | wwPDB validaton report |
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Full document | 1xe0_full_validation.pdf.gz | 535.9 KB | Display | |
Data in XML | 1xe0_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 1xe0_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/1xe0 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/1xe0 | HTTPS FTP |
-Related structure data
Related structure data | 1xb9SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12351.986 Da / Num. of mol.: 10 / Fragment: N-terminal core (residues 16-124) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pPep-T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07222 #2: 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: 1.9 Å3/Da / Density % sol: 35 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, Ethylene glycol, Tris-HCl, Magnesium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2004 / Details: Mirrors |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→90 Å / Num. obs: 109907 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.03 / Rsym value: 0.031 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.2 / Num. unique all: 706 / Rsym value: 0.155 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XB9 Resolution: 1.7→84.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.936 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.142 / 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: 23.185 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→84.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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