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Yorodumi- PDB-4ut0: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ut0 | ||||||
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Title | THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7) | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / CATALYSIS / PROTEIN-DNA INTERACTION | ||||||
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. / Stella, S. / Redondo, P. / Gomez, H. / Marcaida, M.J. / Orozco, M. / Prieto, J. / Montoya, G. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ut0.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ut0.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 4ut0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ut0_validation.pdf.gz | 502.7 KB | Display | wwPDB validaton report |
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Full document | 4ut0_full_validation.pdf.gz | 512.5 KB | Display | |
Data in XML | 4ut0_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 4ut0_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4ut0 ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4ut0 | HTTPS FTP |
-Related structure data
Related structure data | 4d6nC 4d6oC 4un7C 4un8C 4un9C 4unaC 4unbC 4uncC 2vs8S 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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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: 23265.057 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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, 110 molecules
#6: Chemical | ChemComp-MN / #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: 2.33 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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.65 |
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: 2.4→46.49 Å / Num. obs: 54032 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 53.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VS8 Resolution: 2.4→46.489 Å / SU ML: 0.31 / σ(F): 0.05 / Phase error: 26.47 / 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→46.489 Å
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Refine LS restraints |
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LS refinement shell |
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