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- PDB-4un8: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4un8 | ||||||
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Title | THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2) | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / DNA-BINDING PROTEIN / CATALYSIS / PROTEIN-DNA INTERACTION | ||||||
Function / homology | ![]() intein-mediated protein splicing / intron homing / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Molina, R. / Stella, S. / Redondo, P. / Gomez, H. / Marcaida, M.J. / Orozco, M. / Prieto, J. / Montoya, G. | ||||||
![]() | ![]() Title: Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease. Authors: Molina, R. / Stella, S. / Redondo, P. / Gomez, H. / Marcaida, M.J. / Orozco, M. / Prieto, J. / Montoya, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.8 KB | Display | ![]() |
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PDB format | ![]() | 162.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.1 KB | Display | ![]() |
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Full document | ![]() | 482.2 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d6nC ![]() 4d6oC ![]() 4un7C ![]() 4un9C ![]() 4unaC ![]() 4unbC ![]() 4uncC ![]() 4ut0C ![]() 2vs7S ![]() 4un6 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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
-HOMING ENDONUCLEASE I- ... , 2 types, 3 molecules ADG
#1: Protein | Mass: 23265.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21505, Hydrolases; Acting on ester bonds #4: Protein | | Mass: 23280.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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 , 2 types, 164 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.65 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.64 Å / Num. obs: 42078 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 52.87 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VS7 Resolution: 2.6→46.642 Å / SU ML: 0.32 / σ(F): 1.12 / Phase error: 22.96 / 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: 2.6→46.642 Å
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Refine LS restraints |
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LS refinement shell |
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