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- PDB-4d6o: 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: 4d6o | ||||||
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Title | THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MG (STATE 2) | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / CATALYSIS / PROTEIN-DNA INTERACTION / X-RAY CRYSTALLOGRAPHY. | ||||||
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 | ![]() | 216.7 KB | Display | ![]() |
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PDB format | ![]() | 165.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.8 KB | Display | ![]() |
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Full document | ![]() | 496.5 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d6nC ![]() 4un7C ![]() 4un8C ![]() 4un9C ![]() 4unaC ![]() 4unbC ![]() 4uncC ![]() 4ut0C ![]() 2vs7S 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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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: 23265.057 Da / Num. of mol.: 3 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 , 4 types, 6 molecules BHCIEF
#2: DNA chain | Mass: 7707.932 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 7654.926 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: DNA chain | | Mass: 7691.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #5: DNA chain | | Mass: 7669.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 3 types, 266 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.49 Å / Num. obs: 70363 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB DENTRY 2VS7 Resolution: 2.2→46.489 Å / SU ML: 0.25 / σ(F): 1.11 / Phase error: 24.02 / 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: 2.2→46.489 Å
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Refine LS restraints |
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LS refinement shell |
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