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- PDB-4k4h: Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN CO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k4h | ||||||
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Title | Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. | ||||||
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![]() | TRANSFERASE/DNA / DNA POLYMERASE / DNA REPAIR / PHOSPHORYL TRANSFER REACTION / 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 | ![]() ![]() ![]() | ||||||
![]() | Vyas, R. / Suo, Z. | ||||||
![]() | ![]() Title: Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda. Authors: Vyas, R. / Zahurancik, W.J. / Suo, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331.9 KB | Display | ![]() |
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PDB format | ![]() | 262.7 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules AEIM
#1: Protein | Mass: 38254.574 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: CHAIN A, E, I, M / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 3 types, 12 molecules BFJNCGKODHLP
#2: DNA chain | Mass: 3390.209 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: CHAIN E / Source: (gene. exp.) ![]() ![]() ![]() #3: DNA chain | Mass: 1793.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: CHAIN I / Source: (gene. exp.) ![]() ![]() ![]() #4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: CHAIN M / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 523 molecules ![](data/chem/img/1RZ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-1RZ / #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-ACT / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Mar 13, 2013 |
Radiation | Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.88 Å / Num. obs: 112509 / % possible obs: 96.1 % |
Reflection shell | Resolution: 2.1→2.14 Å / % possible all: 89.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.084 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.88 Å
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Refine LS restraints |
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