+Open data
-Basic information
Entry | Database: PDB / ID: 2vs7 | ||||||
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Title | The crystal structure of I-DmoI in complex with DNA and Ca | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / PROTEIN/NUCLEIC ACID CRYSTALLOGRAPHY / ENDONUCLEASE / MEGANUCLEASE / INTRON HOMING / GENOME ENGINEERING / DNA-BINDING PROTEIN / NUCLEASE / HYDROLASE / MAGNESIUM / GENE THERAPY | ||||||
Function / homology | Function and homology information intron homing / intein-mediated protein splicing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | DESULFUROCOCCUS MOBILIS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
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. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vs7.cif.gz | 402.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vs7.ent.gz | 337.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vs7 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vs7 | HTTPS FTP |
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-Related structure data
Related structure data | 2vs8C 2vs9 C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ADG
#1: Protein | Mass: 23265.057 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSSETA (DE3) PLYSS References: UniProt: P21505, Hydrolases; Acting on ester bonds |
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-DNA chain , 2 types, 6 molecules BEHCFI
#2: DNA chain | Mass: 7707.932 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DESULFUROCOCCUS MOBILIS (archaea) #3: DNA chain | Mass: 7654.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DESULFUROCOCCUS MOBILIS (archaea) |
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-Non-polymers , 3 types, 614 molecules
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.67 % / Description: NONE |
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Crystal grow | Details: 5.6% PEG 4000, 0.07M SODIUM ACETATE, 30% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9, 1.5414 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→25 Å / Num. obs: 87351 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9 | |||||||||
Reflection shell | Highest resolution: 2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.05→25.76 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.157 / 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: 46.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→25.76 Å
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Refine LS restraints |
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