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Yorodumi- PDB-5dtu: Crystal structure of the RNA-helicase Prp28 from Chaetomium therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dtu | ||||||
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Title | Crystal structure of the RNA-helicase Prp28 from Chaetomium thermophilum bound to ADP | ||||||
Components | Prp28 | ||||||
Keywords | HYDROLASE / DEAD-box Protein / ATPase / RNA-helicase / DDX23 | ||||||
Function / homology | Function and homology information helicase activity / nucleic acid binding / hydrolase activity / ATP binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.199 Å | ||||||
Authors | Tauchert, M.J. / Ficner, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Structural analysis of the spliceosomal RNA helicase Prp28 from the thermophilic eukaryote Chaetomium thermophilum. Authors: Tauchert, M.J. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dtu.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dtu.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/5dtu ftp://data.pdbj.org/pub/pdb/validation_reports/dt/5dtu | HTTPS FTP |
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-Related structure data
Related structure data | 4nhoS 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: 52963.598 Da / Num. of mol.: 1 / Fragment: UNP residues 238-709 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_0054430 / Plasmid: pPSG-IBA25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SBQ7 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 200 mM NaCl, 20 % (w/v) PEG 4000, 100 mM Tris pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 3.199→45.7734 Å / Num. obs: 8454 / % possible obs: 95.1 % / Redundancy: 3.58 % / Biso Wilson estimate: 68.9 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.17 |
Reflection shell | Resolution: 3.199→3.299 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.45 / Num. measured obs: 2660 / Num. unique all: 723 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4nho Resolution: 3.199→45.7734 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.199→45.7734 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -36.7276 Å / Origin y: 20.4106 Å / Origin z: 15.8747 Å
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Refinement TLS group | Selection details: chain A |