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Yorodumi- PDB-6fa5: CRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 IN COMPLEX WITH ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fa5 | ||||||
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Title | CRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 IN COMPLEX WITH ADP | ||||||
Components | Putative mRNA splicing factor | ||||||
Keywords | HYDROLASE / SPLICING / ATPASE / HELICASE / G-PATCH | ||||||
Function / homology | Function and homology information catalytic step 2 spliceosome / RNA splicing / helicase activity / mRNA processing / hydrolase activity / RNA helicase / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.303 Å | ||||||
Authors | Hamann, F. / Schmitt, A. / Neumann, P. / Ficner, R. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Crystal structure of the spliceosomal DEAH-box ATPase Prp2. Authors: Schmitt, A. / Hamann, F. / Neumann, P. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fa5.cif.gz | 267.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fa5.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 6fa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fa5_validation.pdf.gz | 774 KB | Display | wwPDB validaton report |
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Full document | 6fa5_full_validation.pdf.gz | 780.1 KB | Display | |
Data in XML | 6fa5_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6fa5_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/6fa5 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6fa5 | HTTPS FTP |
-Related structure data
Related structure data | 6fa9C 6faaSC 6facC 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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Unit cell |
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-Components
#1: Protein | Mass: 70835.133 Da / Num. of mol.: 1 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_0063660 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SEG4 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-PEG / |
#5: 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: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 100mM Na-HEPES, 250mM NaCl, 25% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Aug 31, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→44.638 Å / Num. obs: 30007 / % possible obs: 99.1 % / Redundancy: 4.282 % / Biso Wilson estimate: 49.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.09 / Χ2: 1.077 / Net I/σ(I): 13.78 / Num. measured all: 128483 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FAA Resolution: 2.303→44.638 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.3 Å2 / Biso mean: 58.15 Å2 / Biso min: 26.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.303→44.638 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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