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- PDB-2bcq: DNA polymerase lambda in complex with a DNA duplex containing an ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bcq | ||||||
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Title | DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp | ||||||
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![]() | Transferase / Lyase/DNA / misalignment / extrahelical / mutagenesis / mutation / deletion / streisinger / slippage / 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: Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Pedersen, L.C. / Kunkel, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 78.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.3 KB | Display | ![]() |
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Full document | ![]() | 473.8 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bcrC ![]() 2bcsC ![]() 2bcuC ![]() 2bcvC ![]() 1rztS 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 DPT
#1: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template |
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#2: DNA chain | Mass: 2122.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer |
#3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Downstream primer |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 37479.750 Da / Num. of mol.: 1 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 , 5 types, 576 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-PPV / | #8: Chemical | ChemComp-EDO / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96318 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 57189 / Num. obs: 57247 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.3 Å2 |
Reflection shell | Resolution: 1.65→1.71 Å / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1RZT Resolution: 1.65→41.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 562564.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.4894 Å2 / ksol: 0.32173 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→41.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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