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- PDB-6bdb: I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bdb | ||||||
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Title | I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) | ||||||
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![]() | HYDROLASE / Nucleic Acid | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Brown, C. / Zhang, K. / McMurrough, T.A. / Laforet, M. / Gloor, G.B. / Edgell, D.R. / Junop, M. | ||||||
![]() | ![]() Title: I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) Authors: Laforet, M. / McMurrough, T.A. / Brown, C. / Junop, M. / Zhang, K. / Gloor, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.1 KB | Display | ![]() |
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PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 442 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35136.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HEG fusion, rps3 / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 7775.014 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
#3: DNA chain | Mass: 8198.330 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M DiAmmonium Phosphate 20% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→66.74 Å / Num. obs: 80496 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.056 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.5→1.517 Å / Rpim(I) all: 0.327 |
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Processing
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Refinement | Resolution: 1.5→42.019 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97 / 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: 1.5→42.019 Å
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Refine LS restraints |
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LS refinement shell |
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