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- PDB-5a72: Crystal structure of the homing endonuclease I-CvuI in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a72 | ||||||
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Title | Crystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Ca | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES | ||||||
Function / homology | ![]() intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Molina, R. / Redondo, P. / LopezMendez, B. / Villate, M. / Merino, N. / Blanco, F.J. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G. | ||||||
![]() | ![]() Title: Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification Authors: Molina, R. / Redondo, P. / Lopez-Mendez, B. / Villate, M. / Merino, N. / Blanco, F.J. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, 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 | ![]() | 104.4 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
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Full document | ![]() | 438.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a74C ![]() 5a77C ![]() 5a78C ![]() 1g9yS ![]() 5a73 ![]() 5a75 C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 19278.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P56347, Hydrolases; Acting on ester bonds #2: DNA chain | Mass: 7369.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.1 Å / Num. obs: 14572 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 33.18 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G9Y Resolution: 2.6→47.105 Å / SU ML: 0.33 / σ(F): 1.26 / Phase error: 26.4 / 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: 2.6→47.105 Å
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Refine LS restraints |
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LS refinement shell |
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