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Yorodumi- PDB-4aaf: Crystal structure of the mutant D75N I-CreI in complex with an al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aaf | ||||||
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Title | Crystal structure of the mutant D75N I-CreI in complex with an altered target (The four central bases, 2NN region, are composed by TGCA from 5' to 3') | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES | ||||||
Function / homology | Function and homology information intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | CHLAMYDOMONAS REINHARDTII (plant) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Molina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Epinat, J.C. / Valton, J. / Grizot, S. / Duchateau, P. ...Molina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Epinat, J.C. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage. Authors: Molina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Charles Epinat, 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 | 4aaf.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aaf.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 4aaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aaf ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aaf | HTTPS FTP |
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-Related structure data
Related structure data | 4aabC 4aadC 4aaeC 4aagC 2xe0S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17515.137 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P05725, Hydrolases; Acting on ester bonds #2: DNA chain | Mass: 7368.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 3.05 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 35% METOH, 0.1M SODIUM CACODYLATE PH 6.5, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→71.43 Å / Num. obs: 21522 / % possible obs: 98.3 % / Observed criterion σ(I): 1.6 / Redundancy: 3.5 % / Biso Wilson estimate: 56.63 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XE0 Resolution: 2.5→55.144 Å / SU ML: 0.84 / σ(F): 1.33 / Phase error: 27.38 / 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 / Bsol: 52.934 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→55.144 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.9731 Å / Origin y: -9.0236 Å / Origin z: 24.1792 Å
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Refinement TLS group | Selection details: ALL |