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- PDB-1xsp: Crystal Structure of human DNA polymerase lambda in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xsp | ||||||
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Title | Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate | ||||||
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![]() | TRANSFERASE/DNA / DNA POLYMERASE LAMBDA / Protein-DNA complex / Helix-hairpin-helix / TRANSFERASE-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. / Kunkel, T.A. / Pedersen, L.C. | ||||||
![]() | ![]() Title: A closed conformation for the Pol lambda catalytic cycle. Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Kunkel, T.A. / Pedersen, L.C. #1: ![]() Title: A Structural Solution for the DNA Polymerase-lambda Dependent Repair of DNA Gaps with Minimal Homology Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Blanco, L. / Kunkel, T.A. / Pedersen, L.C. #2: ![]() Title: DNA polymerase lambda, a novel DNA repair enzyme in human cells Authors: Garcia-Diaz, M. / Bebenek, K. / Sabariegos, R. / Dominguez, O. / Rodriguez, J. / Kirchhoff, T. / Garcia-Palomero, E. / Picher, A.J. / Juarez, R. / Ruiz, J.F. / Kunkel, T.A. / Blanco, L. #3: ![]() Title: The frameshift Infidelity of human DNA polymerase lambda. Implications for function. Authors: Bebenek, K. / Garcia-Diaz, K. / Blanco, L. / Kunkel, T.A. #4: ![]() Title: Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in Base Excision Repair Authors: Garcia-Diaz, M. / Bebenek, K. / Kunkel, T.A. / Blanco, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.4 KB | Display | ![]() |
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PDB format | ![]() | 73.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The protein is a monomer thus the asymmetric unit represents the biological unit |
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Components
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA |
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#2: DNA chain | Mass: 2122.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA |
#3: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Downstream Primer DNA |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 37447.688 Da / Num. of mol.: 1 / Fragment: 39 kDa catalytic C-terminal domain / Mutation: C543A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 339 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-PPV / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2-propanol, sodium citrate, sodium chloride, cacodylate, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 25700 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.114 / Net I/σ(I): 16.23 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.1 % / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7143 Å2 / ksol: 0.308968 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→41.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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