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Yorodumi- PDB-5o9e: Crystal structure of the Imp4-Mpp10 complex from Chaetomium therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o9e | ||||||
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Title | Crystal structure of the Imp4-Mpp10 complex from Chaetomium thermophilum | ||||||
Components |
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Keywords | RIBOSOME / Ribosome biogenesis / BRIX | ||||||
Function / homology | Function and homology information Mpp10 complex / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / snoRNA binding / small-subunit processome / rRNA processing Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.884 Å | ||||||
Authors | Kharde, S. / Ahmed, Y.L. / Sinning, I. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. Authors: Sa-Moura, B. / Kornprobst, M. / Kharde, S. / Ahmed, Y.L. / Stier, G. / Kunze, R. / Sinning, I. / Hurt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o9e.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o9e.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o9e_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 5o9e_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 5o9e_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5o9e_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9e ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9e | HTTPS FTP |
-Related structure data
Related structure data | 5by8S S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 22800.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0062900 / Plasmid: pET21g / Details (production host): modified pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SE90 |
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#2: Protein | Mass: 14787.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0046030 / Plasmid: pETZZ1a / Details (production host): modified pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S9I7 |
#3: Chemical | ChemComp-EDO / |
#4: 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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20-30 % Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→48.883 Å / Num. obs: 26155 / % possible obs: 99.98 % / Redundancy: 7 % / Biso Wilson estimate: 27.64 Å2 / Net I/σ(I): 9.15 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BY8 Resolution: 1.884→48.883 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.75 Å2 / Biso mean: 35.1536 Å2 / Biso min: 14.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.884→48.883 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 30.5593 Å / Origin y: 23.2614 Å / Origin z: 33.8023 Å
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Refinement TLS group |
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