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Yorodumi- PDB-5o6g: Structures and dynamics of mesophilic variants from the homing en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o6g | ||||||
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Title | Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Desulfurococcus mobilis | ||||||
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 mucosus (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Molina, R. / Marcaida, M.J. | ||||||
Citation | Journal: J. Comput. Aided Mol. Des. / Year: 2017 Title: Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI. Authors: Alba, J. / Marcaida, M.J. / Prieto, J. / Montoya, G. / Molina, R. / D'Abramo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o6g.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o6g.ent.gz | 159.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o6g_validation.pdf.gz | 482.4 KB | Display | wwPDB validaton report |
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Full document | 5o6g_full_validation.pdf.gz | 494.5 KB | Display | |
Data in XML | 5o6g_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 5o6g_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/5o6g ftp://data.pdbj.org/pub/pdb/validation_reports/o6/5o6g | HTTPS FTP |
-Related structure data
Related structure data | 5o6iC 4un8S 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ADG
#1: Protein | Mass: 23445.240 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfurococcus mucosus (archaea) / Production host: Escherichia coli (E. coli) References: UniProt: P21505, Hydrolases; Acting on ester bonds |
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-DNA chain , 2 types, 6 molecules BEHCFI
#2: DNA chain | Mass: 7707.932 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 7654.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 59 molecules
#4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CL / | #6: 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: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→93.1 Å / Num. obs: 35510 / % possible obs: 97.5 % / Redundancy: 4.7 % / Net I/σ(I): 9.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UN8 Resolution: 2.75→56.184 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→56.184 Å
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Refine LS restraints |
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LS refinement shell |
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