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- PDB-2pfq: Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pfq | ||||||
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Title | Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal | ||||||
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![]() | Transferase / lyase/DNA / DNA polymerase / DNA Repair / phosphoryl transfer reaction / manganese / lyase-DNA COMPLEX | ||||||
Function / homology | ![]() DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Pedersen, L.C. / Kunkel, T.A. | ||||||
![]() | ![]() Title: Role of the catalytic metal during polymerization by DNA polymerase lambda. Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Pedersen, L.C. / Kunkel, T.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.6 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.6 KB | Display | ![]() |
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Full document | ![]() | 823.3 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pfnC ![]() 2pfoC ![]() 2pfpC ![]() 1xsnS C: citing same article ( 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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Components
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 3390.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#2: DNA chain | Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 37447.688 Da / Num. of mol.: 1 / Mutation: C543A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 6 types, 237 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / | ||||||||
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#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-DCP / | #9: Chemical | ChemComp-PPV / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.08 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Jun 27, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 26491 / % possible obs: 88.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Χ2: 1.36 / Net I/σ(I): 24.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XSN Resolution: 2.1→50 Å / σ(F): 0 Details: Conformation A in the coordinates corresponds to the post-catalytic state, while conformation B corresponds to the pre-catalytic state.
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Solvent computation | Bsol: 67.771 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.427 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Xplor file |
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