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Open data
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Basic information
Entry | Database: PDB / ID: 3c0l | ||||||
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Title | UVDE K229R | ||||||
![]() | UV endonuclease | ||||||
![]() | HYDROLASE / UVDE / TIM barrel / endonuclease / DNA repair / Plasmid | ||||||
Function / homology | ![]() response to UV / nucleotide-excision repair / endonuclease activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meulenbroek, E.M. / Paspaleva, K. / Thomassen, E.A.J. / Abrahams, J.P. / Goosen, N. / Pannu, N.S. | ||||||
![]() | ![]() Title: Involvement of a carboxylated lysine in UV damage endonuclease Authors: Meulenbroek, E.M. / Paspaleva, K. / Thomassen, E.A. / Abrahams, J.P. / Goosen, N. / Pannu, N.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.9 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.1 KB | Display | ![]() |
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Full document | ![]() | 430.6 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bzgSC ![]() 3bzjC ![]() 3c0qC ![]() 3c0sC 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
#1: Protein | Mass: 34011.664 Da / Num. of mol.: 1 / Mutation: L133I, K229R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M Acetate, pH5.6, 1M Naformate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR225 / Detector: CCD / Date: Jul 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→46.18 Å / Num. all: 5706 / Num. obs: 5367 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 3.15→3.32 Å / Redundancy: 11 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 6.6 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BZG Resolution: 3.15→46.18 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.855 / SU B: 20.921 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.563 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→46.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.232 Å / Total num. of bins used: 20
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