+Open data
-Basic information
Entry | Database: PDB / ID: 2vs8 | ||||||
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Title | The crystal structure of I-DmoI in complex with DNA and Mn | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / MEGANUCLEASE / INTRON HOMING / GENETIC ENGINEERING / HOMING ENDONUCLEASE / PROTEIN/DNA CRYSTALLOGRAPHY / NUCLEASE / HYDROLASE / MAGNESIUM / ENDONUCLEASE / DNA-BINDING PROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 2vs8.cif.gz | 404.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vs8.ent.gz | 321.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vs8 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vs8 | HTTPS FTP |
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-Related structure data
Related structure data | 2vs7SC 2vs9 S: Starting model for refinement 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 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.) 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 , 4 types, 12 molecules BGLCHMDINEJO
#2: DNA chain | Mass: 4296.791 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DESULFUROCOCCUS MOBILIS (archaea) #3: DNA chain | Mass: 3366.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DESULFUROCOCCUS MOBILIS (archaea) #4: DNA chain | Mass: 4554.962 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DESULFUROCOCCUS MOBILIS (archaea) #5: DNA chain | Mass: 3055.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DESULFUROCOCCUS MOBILIS (archaea) |
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-Non-polymers , 3 types, 401 molecules
#6: Chemical | ChemComp-MN / #7: Chemical | #8: 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: 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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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