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Yorodumi- PDB-6fb6: Crystal Structure of a Tailored I-CreI Homing Endonuclease Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fb6 | ||||||
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Title | Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Manganese | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Chlamydomonas reinhardtii | ||||||
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: 2.6 Å | ||||||
Authors | Molina, R. / Prieto, J. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Understanding the indirect DNA read-out specificity of I-CreI Meganuclease. Authors: Prieto, J. / Redondo, P. / Lopez-Mendez, B. / D'Abramo, M. / Merino, N. / Blanco, F.J. / Duchateau, P. / Montoya, G. / Molina, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fb6.cif.gz | 191.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fb6.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fb6 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fb6 | HTTPS FTP |
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-Related structure data
Related structure data | 6fb0C 6fb1C 6fb2C 6fb5C 6fb7C 6fb8C 6fb9C 1g9zS 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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1 |
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Unit cell |
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-Components
-I-CreI monomer ... , 2 types, 2 molecules AB
#1: Protein | Mass: 17528.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P05725*PLUS |
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#2: Protein | Mass: 17583.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P05725*PLUS |
-DNA chain , 4 types, 4 molecules DFEG
#3: DNA chain | Mass: 4215.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 4262.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 3134.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: DNA chain | Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 14 molecules
#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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.6 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.89 Å / Num. obs: 28700 / % possible obs: 96.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 0.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G9Z Resolution: 2.6→44.89 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→44.89 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: 38.3742 Å / Origin y: 12.482 Å / Origin z: 185.1541 Å
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Refinement TLS group | Selection details: all |