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- PDB-2vbn: Molecular basis of human XPC gene recognition and cleavage by eng... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vbn | ||||||
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Title | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | ||||||
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![]() | HYDROLASE / UV-INDUCED DNA DAMAGE / CUTTING DNA ENDONUCLEASES / ENDONUCLEASE / INTRON HOMING / INI3- 4_MAGNESIUM / PLASTID / NUCLEASE / CHLOROPLAST / DOUBLE STRAND BREAK (DSB) / HOMING ENDONUCLEASES (HES) | ||||||
Function / homology | ![]() intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Redondo, P. / Prieto, J. / Munoz, I.G. / Alibes, A. / Stricher, F. / Serrano, L. / Arnould, S. / Perez, C. / Cabaniols, J.P. / Duchateau, P. ...Redondo, P. / Prieto, J. / Munoz, I.G. / Alibes, A. / Stricher, F. / Serrano, L. / Arnould, S. / Perez, C. / Cabaniols, J.P. / Duchateau, P. / Paques, F. / Blanco, F.J. / Montoya, G. | ||||||
![]() | ![]() Title: Molecular Basis of Xeroderma Pigmentosum Group C DNA Recognition by Engineered Meganucleases Authors: Redondo, P. / Prieto, J. / Munoz, I.G. / Alibes, A. / Stricher, F. / Serrano, L. / Cabaniols, J.P. / Daboussi, F. / Arnould, S. / Perez, C. / Duchateau, P. / Paques, F. / Blanco, F.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 | ![]() | 207.1 KB | Display | ![]() |
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PDB format | ![]() | 160.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 477.6 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vbjC ![]() 2vblC ![]() 2vboC ![]() 1g9zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA ENDONUCLEASE I- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 17529.184 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P05725, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 17578.250 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P05725, Hydrolases; Acting on ester bonds |
-DNA chain , 4 types, 4 molecules CEST
#3: DNA chain | Mass: 4254.791 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#4: DNA chain | Mass: 4227.749 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#5: DNA chain | Mass: 3111.082 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#6: DNA chain | Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 353 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.37 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 4 MG/ML PROTEIN, 20% PEG1000, 0.1M IMIDAZOLE PH 8.0, 0.2 M CAAC2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.872 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.13 Å / Num. obs: 33531 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G9Z Resolution: 1.9→46.13 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.777 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.13 Å
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Refine LS restraints |
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