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- PDB-5irf: Reverse transcriptase domain of group II intron maturase from Ros... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5irf | ||||||
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Title | Reverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P1 space group | ||||||
![]() | Retron-type reverse transcriptase | ||||||
![]() | RNA BINDING PROTEIN / Group II intron / maturase / reverse transcriptase | ||||||
Function / homology | ![]() RNA-directed DNA polymerase activity / defense response to virus / RNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, C. / Pyle, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Authors: Zhao, C. / Pyle, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349.7 KB | Display | ![]() |
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PDB format | ![]() | 289.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
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Full document | ![]() | 454 KB | Display | |
Data in XML | ![]() | 51 KB | Display | |
Data in CIF | ![]() | 75.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hhjSC ![]() 5hhkC ![]() 5hhlC ![]() 5irgC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 34918.109 Da / Num. of mol.: 4 / Fragment: UNP residues 1-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: RO1_37670 / Production host: ![]() ![]() #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Bis-Tris propane pH 8.5, 200 mM NaOAc-3H2O, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.47 Å / Num. obs: 152938 / % possible obs: 96.1 % / Redundancy: 3.9 % / Net I/σ(I): 19.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HHJ Resolution: 1.6→46.47 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.94 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→46.47 Å
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Refine LS restraints |
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LS refinement shell |
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