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Open data
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Basic information
Entry | Database: PDB / ID: 2vs8 | ||||||
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Title | The crystal structure of I-DmoI in complex with DNA and Mn | ||||||
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![]() | DNA BINDING PROTEIN / MEGANUCLEASE / INTRON HOMING / GENETIC ENGINEERING / HOMING ENDONUCLEASE / PROTEIN/DNA CRYSTALLOGRAPHY / NUCLEASE / HYDROLASE / MAGNESIUM / ENDONUCLEASE / DNA-BINDING PROTEIN | ||||||
Function / homology | ![]() intein-mediated protein splicing / intron homing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marcaida, M.J. / Prieto, J. / Redondo, P. / Nadra, A.D. / Alibes, A. / Serrano, L. / Grizot, S. / Duchateau, P. / Paques, F. / Blanco, F.J. / Montoya, G. | ||||||
![]() | ![]() Title: Crystal Structure of I-Dmoi in Complex with its Target DNA Provides New Insights Into Meganuclease Engineering. Authors: Marcaida, M.J. / Prieto, J. / Redondo, P. / Nadra, A.D. / Alibes, A. / Serrano, L. / Grizot, S. / Duchateau, P. / Paques, F. / Blanco, F.J. / Montoya, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 404.2 KB | Display | ![]() |
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PDB format | ![]() | 321.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 527.9 KB | Display | ![]() |
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Full document | ![]() | 552.9 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vs7SC ![]() 2vs9 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules AFK
#1: Protein | Mass: 23396.254 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21505, Hydrolases; Acting on ester bonds |
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-DNA chain , 4 types, 12 molecules BGLCHMDINEJO
#2: DNA chain | Mass: 4296.791 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | Mass: 3366.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 4554.962 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #5: DNA chain | Mass: 3055.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 401 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MN / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 73.5 % / Description: NONE |
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Crystal grow | Details: 5.6% PEG 4000, 0.07M SODIUM ACETATE, PH 4.6-5.5, 30% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26.82 Å / Num. obs: 80887 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VS7 Resolution: 2.1→25.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.171 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→25.76 Å
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Refine LS restraints |
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