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Yorodumi- PDB-5a74: Crystal structure of the homing endonuclease I-CvuI in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a74 | ||||||
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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 Mn | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES | ||||||
Function / homology | Function and homology information intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | CHLORELLA VULGARIS (plant) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Molina, R. / Redondo, P. / LopezMendez, B. / Villate, M. / Merino, N. / Blanco, F.J. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a74.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a74.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/5a74 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/5a74 | HTTPS FTP |
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-Related structure data
Related structure data | 5a72C 5a77C 5a78C 1g9yS 5a73 5a75 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19292.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLORELLA VULGARIS (plant) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: P56347, Hydrolases; Acting on ester bonds #2: DNA chain | Mass: 4264.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 3060.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: Chemical | #5: 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: 2.43 Å3/Da / Density % sol: 55 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.8 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→62.63 Å / Num. obs: 17475 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 36.29 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G9Y Resolution: 2.5→61.944 Å / SU ML: 0.26 / σ(F): 0.97 / Phase error: 33.23 / 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: 2.5→61.944 Å
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Refine LS restraints |
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LS refinement shell |
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