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- PDB-5dmp: Structure of the Archaeal NHEJ Phosphoesterase from Methanocella ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dmp | ||||||
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Title | Structure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola. | ||||||
![]() | Uncharacterized protein | ||||||
![]() | HYDROLASE / Archaeal Proteins / Biocatalysis / DNA Repair Enzymes / Phosphoric Diester Hydrolases / Phosphoric Monoester Hydrolases | ||||||
Function / homology | DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / oxido(dioxo)vanadium / LigD_N domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Brissett, N.C. / Bartlett, E.J. / Doherty, A.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for DNA strand displacement by NHEJ repair polymerases. Authors: Bartlett, E.J. / Brissett, N.C. / Plocinski, P. / Carlberg, T. / Doherty, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.6 KB | Display | ![]() |
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PDB format | ![]() | 35.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.8 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dmuC ![]() 3n9bS 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: 19062.793 Da / Num. of mol.: 1 / Fragment: UNP residues 30-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-VN4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM magnesium sulfate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 27, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.793→49.424 Å / Num. all: 18976 / Num. obs: 18976 / % possible obs: 98.9 % / Redundancy: 5 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.056 / Rsym value: 0.05 / Net I/av σ(I): 8.17 / Net I/σ(I): 16.4 / Num. measured all: 95174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 32.66 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3n9b Resolution: 1.793→49.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.1838 / FOM work R set: 0.8475 / SU B: 2.571 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1092 / SU Rfree: 0.1057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.83 Å2 / Biso mean: 37.484 Å2 / Biso min: 21.38 Å2
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Refinement step | Cycle: final / Resolution: 1.793→49.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.793→1.84 Å / Total num. of bins used: 20
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