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- PDB-3eh8: Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eh8 | ||||||
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Title | Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium | ||||||
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![]() | HYDROLASE/DNA / Protein-DNA complex / Endonuclease / Hydrolase / Intron homing / Mitochondrion / mRNA processing / mRNA splicing / Nuclease / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() intron homing / RNA splicing / mRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeuchi, R. / Stoddard, B.L. | ||||||
![]() | ![]() Title: Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Authors: Takeuchi, R. / Certo, M. / Caprara, M.G. / Scharenberg, A.M. / Stoddard, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.8 KB | Display | ![]() |
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PDB format | ![]() | 205.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.3 KB | Display | ![]() |
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Full document | ![]() | 533.5 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p8kS 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29611.490 Da / Num. of mol.: 3 / Fragment: Y2 I-AniI (UNP residues 237-488) / Mutation: F13Y, F80K, S111Y, L232K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P03880, Hydrolases; Acting on ester bonds #2: DNA chain | Mass: 9609.168 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: the physiological DNA target site of I-AniI in the mitochondrial apocytochrome B gene of A. nidulans #3: DNA chain | Mass: 9458.087 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: the physiological DNA target site of I-AniI in the mitochondrial apocytochrome B gene of A. nidulans #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.13 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 32% Polypropylene glycol P400, 0.08M Bis-Tris, 0.25M sodium chloride, 0.05M calucium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Detector: CCD / Date: Jun 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→37.14 Å / Num. all: 46294 / Num. obs: 44303 / % possible obs: 95.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.25 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1P8K Resolution: 2.7→37.14 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 27.67 / SU ML: 0.268 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.305 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→37.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.703→2.772 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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