+Open data
-Basic information
Entry | Database: PDB / ID: 4ynw | ||||||
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Title | Assembly Chaperone of RpL4 (Acl4) (Residues 1-338) | ||||||
Components | ACL4 | ||||||
Keywords | CHAPERONE / ribosome assembly / nucleocytoplasmic transport / tetratricopeptide repeat | ||||||
Function / homology | Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Huber, F.M. / Hoelz, A. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension. Authors: Stelter, P. / Huber, F.M. / Kunze, R. / Flemming, D. / Hoelz, A. / Hurt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ynw.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ynw.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ynw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ynw_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 4ynw_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 4ynw_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4ynw_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/4ynw ftp://data.pdbj.org/pub/pdb/validation_reports/yn/4ynw | HTTPS FTP |
-Related structure data
Related structure data | 4ynvSC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38085.727 Da / Num. of mol.: 2 / Fragment: UNP residues 1-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0010130 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0I4 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 % (w/v) PEG 3350, 0.2 M ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97939 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 16367 / % possible obs: 97.2 % / Redundancy: 7.7 % / Rsym value: 0.046 / Net I/σ(I): 40.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YNV Resolution: 2.95→19.616 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.39 / 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: 2.95→19.616 Å
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Refine LS restraints |
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LS refinement shell |
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