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Yorodumi- PDB-5cxc: Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cxc | ||||||
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Title | Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group | ||||||
Components |
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Keywords | PROTEIN BINDING / ribosome assembly / WD40 / beta-propeller / ubiquitin-like domain | ||||||
Function / homology | Function and homology information PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleoplasm Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Wegrecki, M. / Bravo, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two beta-propellers during the assembly of large ribosomal subunits in eukaryotes. Authors: Wegrecki, M. / Rodriguez-Galan, O. / de la Cruz, J. / Bravo, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cxc.cif.gz | 330.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cxc.ent.gz | 268.5 KB | Display | PDB format |
PDBx/mmJSON format | 5cxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cxc_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 5cxc_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 5cxc_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 5cxc_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxc ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxc | HTTPS FTP |
-Related structure data
Related structure data | 5cxbC 5cykC 3pslS 4u7aS C: citing same article (ref.) 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: 54720.191 Da / Num. of mol.: 1 / Fragment: UNP residues 433-801 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: YTM1, CTHT_0061460 / Plasmid: pOPINF / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SFB5 |
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#2: Protein | Mass: 40919.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: ERB1, CTHT_0057570 / Plasmid: pET28-NKI/LIC 6His/3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: G0SCK6 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5.6 Details: 15% PEG 4000,0.1M Na citrate pH 5.6, 0.2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.82 Å / Num. obs: 24180 / % possible obs: 100 % / Redundancy: 39.1 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 17 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 40.2 % / Rmerge(I) obs: 2.817 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U7A and 3PSL Resolution: 3.1→48.818 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3 / 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: 3.1→48.818 Å
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Refine LS restraints |
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LS refinement shell |
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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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