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- PDB-1odg: Very-short-patch DNA repair endonuclease bound to its reaction pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1odg | ||||||
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Title | Very-short-patch DNA repair endonuclease bound to its reaction product site | ||||||
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![]() | HYDROLASE / DNA REPAIR / ENDONUCLEASE / VERY SHORT PATCH REPAIR / DNA REPAI HYDROLASE / NUCLEASE / ZINC / METAL-BINDING | ||||||
Function / homology | ![]() T/G mismatch-specific endonuclease activity / mismatch repair / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bunting, K.A. / Roe, S.M. / Headley, A. / Brown, T. / Savva, R. / Pearl, L.H. | ||||||
![]() | ![]() Title: Crystal Structure of the Escherichia Coli Dcm Very-Short-Patch DNA Repair Endonuclease Bound to its Reaction Product-Site in a DNA Superhelix Authors: Bunting, K.A. / Roe, S.M. / Headley, A. / Brown, T. / Savva, R. / Pearl, L.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.4 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cw0S 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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Unit cell |
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Details | THE TRIMERIC ASSEMBLY DESCRIBED HERE IS FORMED BYTHE COMPLEX OF PROTEIN CHAIN A WITH DNA CHAINS F,W |
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Components
#1: Protein | Mass: 15568.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: DNA chain | Mass: 3692.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Compound details | FUNCTIONS IN THE DEAMINATION OF 5-METHYLCYTOSINE IN DNA CAUSING MISMATCHES IN T/G WHICH CAN LEAD TO ...FUNCTIONS IN THE DEAMINATIO | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 25 MM HEPES PH7.0, 75 MM NACL, 15% PEG 8000, 50 MM SODIUM CACODYLATE PH 6.5, 75 MM AMMONIUM SULPHATE AND 10% GLYCEROL PROTEIN 2.5 MG/ML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 10084 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 1464 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CW0 Resolution: 2.8→24.7 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.25 Å2 / ksol: 0.318 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→24.7 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.356 / Rfactor Rwork: 0.287 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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