+Open data
-Basic information
Entry | Database: PDB / ID: 5ica | ||||||
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Title | Structure of the CTD complex of UTP12, Utp13, Utp1 and Utp21 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / rRNA processing / 90S preribosome / protein binding | ||||||
Function / homology | Function and homology information small-subunit processome / rRNA processing / ribosome biogenesis / nucleolus Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.507 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 | 5ica.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ica.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ica.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/5ica ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5ica | HTTPS FTP |
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-Related 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: 18434.656 Da / Num. of mol.: 1 / Fragment: UNP residues 769-931 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_0003430 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0RZL9 |
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#2: Protein | Mass: 17371.770 Da / Num. of mol.: 1 / Fragment: UNP residues 738-889 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_0065530 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0SG95 |
#3: Protein | Mass: 27201.953 Da / Num. of mol.: 1 / Fragment: UNP residues 806-1049 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_0037800 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0S872 |
#4: Protein | Mass: 17158.912 Da / Num. of mol.: 1 / Fragment: UNP residues 701-849 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_0061240 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-RIL / References: UniProt: G0SF93 |
Sequence details | ONLY WEAK ELECTRON DENSITY IS OBSERVED FOR RESIDUES 900-911 OF CHAIN C. AND THESE RESIDUES CANNOT ...ONLY WEAK ELECTRON DENSITY IS OBSERVED FOR RESIDUES 900-911 OF CHAIN C. AND THESE RESIDUES CANNOT BE DEFINED EXACTLY. ONLY C-CA ATOMS HAVE BEEN MODELLED. THESE RESIDUES CAN BE ANY POSITION BETWEEN RESIDUES 806-922. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES Sodium, 45% w/v Poly(acrylic acid sodium salt) 5100, 0.02M Magnesium Chloride, 0.01M Spermidine |
-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: Nov 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 34729 / % possible obs: 99.9 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.172 / Rsym value: 0.172 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 20.6 % / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.507→34.382 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.31 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.507→34.382 Å
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Refine LS restraints |
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LS refinement shell |
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