+Open data
-Basic information
Entry | Database: PDB / ID: 5ic7 | ||||||
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Title | Structure of the WD domain of UTP18 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | STRUCTURAL PROTEIN / WD40 / nucleolus / rRNA processing | ||||||
Function / homology | Function and homology information Pwp2p-containing subcomplex of 90S preribosome / small-subunit processome / rRNA processing Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.331 Å | ||||||
Authors | Zhang, C. / Ye, K. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits Authors: Zhang, C. / Sun, Q. / Chen, R. / Chen, X. / Lin, J. / Ye, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ic7.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ic7.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ic7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ic7_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 5ic7_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 5ic7_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5ic7_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/5ic7 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5ic7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46872.977 Da / Num. of mol.: 1 / Fragment: WD domain, UNP residues 197-618 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_0054250 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0SBN9 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 3 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium, 0.1 M sodium chloride, 1.75 M ammonium sulfate and 0.01 M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 10, 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: 2.33→50 Å / Num. obs: 46392 / % possible obs: 99.6 % / Redundancy: 18.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 2.33→2.36 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 20.1 / % possible all: 93.7 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.331→29.153 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.31 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.331→29.153 Å
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Refine LS restraints |
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LS refinement shell |
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