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Yorodumi- PDB-6ar5: Structure of a Thermostable Group II Intron Reverse Transcriptase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ar5 | ||||||
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Title | Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications (Duplex Only) | ||||||
Components |
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Keywords | DNA/RNA / Duplex / DNA-RNA complex | ||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 Å | ||||||
Authors | Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications. Authors: Stamos, J.L. / Lentzsch, A.M. / Lambowitz, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ar5.cif.gz | 26.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ar5.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ar5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/6ar5 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6ar5 | 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: DNA chain | Mass: 3936.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 4479.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: 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: 3.04 Å3/Da / Density % sol: 59.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium malonate, ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.41→36.118 Å / Num. obs: 4275 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.012 / Rrim(I) all: 0.055 / Net I/σ(I): 48 / Num. measured all: 88698 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.413→36.118 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 69.71 Å2 / Biso mean: 39.8353 Å2 / Biso min: 28.64 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.413→36.118 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %
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