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Yorodumi- PDB-4aad: Crystal structure of the mutant D75N I-CreI in complex with its w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aad | ||||||
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Title | Crystal structure of the mutant D75N I-CreI in complex with its wild- type target in absence of metal ions at the active site (The four central bases, 2NN region, are composed by GTAC 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: 3.1 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 | 4aad.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aad.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 4aad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aad_validation.pdf.gz | 466.6 KB | Display | wwPDB validaton report |
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Full document | 4aad_full_validation.pdf.gz | 481.2 KB | Display | |
Data in XML | 4aad_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4aad_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aad ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aad | HTTPS FTP |
-Related structure data
Related structure data | 4aabC 4aaeC 4aafC 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
#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-GOL / #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: 3.36 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 20% PEG300, 0.1M TRIS PH 8.5, 5% PEG8000, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Type: SLS / 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: 3.1→47.44 Å / Num. obs: 12755 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 86.59 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XE0 Resolution: 3.1→47.206 Å / SU ML: 0.67 / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.935 Å2 / ksol: 0.327 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→47.206 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: -15.4485 Å / Origin y: 14.6971 Å / Origin z: -23.2561 Å
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Refinement TLS group | Selection details: ALL |