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Yorodumi- PDB-5akm: THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5akm | ||||||
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Title | THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG | ||||||
Components |
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Keywords | HYDROLASE / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES / X-RAY CRYSTALLOGRAPHY. | ||||||
Function / homology | Function and homology information intein-mediated protein splicing / intron homing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | DESULFUROCOCCUS MOBILIS (archaea) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Molina, R. / Marcaida, M.J. / Redondo, P. / Marenchino, M. / D'Abramo, M. / Montoya, G. / Prieto, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold. Authors: Molina, R. / Marcaida, M.J. / Redondo, P. / Marenchino, M. / Duchateau, P. / D'Abramo, M. / Montoya, G. / Prieto, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5akm.cif.gz | 393.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5akm.ent.gz | 313.9 KB | Display | PDB format |
PDBx/mmJSON format | 5akm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5akm_validation.pdf.gz | 513.9 KB | Display | wwPDB validaton report |
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Full document | 5akm_full_validation.pdf.gz | 520.2 KB | Display | |
Data in XML | 5akm_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 5akm_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/5akm ftp://data.pdbj.org/pub/pdb/validation_reports/ak/5akm | HTTPS FTP |
-Related structure data
Related structure data | 5ak9C 5akfC 5aknC 2vs8S 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules AFK
#1: Protein | Mass: 23295.084 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS References: UniProt: P21505, Hydrolases; Acting on ester bonds |
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-DNA chain , 4 types, 12 molecules BGLCHMDINEJO
#2: DNA chain | Mass: 4296.791 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 3366.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: DNA chain | Mass: 4554.962 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #5: DNA chain | Mass: 3055.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 3 types, 71 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / #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: 3.04 Å3/Da / Density % sol: 60 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / 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: 2.4→50 Å / Num. obs: 97825 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VS8 Resolution: 2.4→46.528 Å / SU ML: 0.3 / σ(F): 0.96 / Phase error: 24.78 / 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: 2.4→46.528 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: 30.3411 Å / Origin y: -0.6391 Å / Origin z: 4.7085 Å
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Refinement TLS group | Selection details: ALL |