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- PDB-3hx0: ternary complex of L277A, H511A, R514 mutant pol lambda bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hx0 | ||||||
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Title | ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA | ||||||
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![]() | TRANSFERASE/DNA / scrunch / X-family / polymerase lambda / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Manganese / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Polymorphism / Transferase / 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. / Larrea, A.A. / Havener, J.M. / Perera, L. / Krahn, J.M. / Pedersen, L.C. / Ramsden, D.A. / Kunkel, T.A. | ||||||
![]() | ![]() Title: Scrunching During DNA Repair Synthesis Authors: Garcia-Diaz, M. / Bebenek, K. / Larrea, A.A. / Havener, J.M. / Perera, L. / Krahn, J.M. / Pedersen, L.C. / Ramsden, D.A. / 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 | ![]() | 311.4 KB | Display | ![]() |
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PDB format | ![]() | 246.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 52.8 KB | Display | |
Data in CIF | ![]() | 71.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hwtS 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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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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Details | Protein functions as monomer |
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Components
-Protein , 1 types, 4 molecules AFKP
#1: Protein | Mass: 37252.426 Da / Num. of mol.: 4 / Fragment: UNP residues 242-575, Catalytic domain / Mutation: L277A, H511A, R514A ,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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-DNA chain , 3 types, 12 molecules BGLQCHMRDINS
#2: DNA chain | Mass: 3671.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized template #3: DNA chain | Mass: 1808.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized primer #4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized downstream primer |
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-Non-polymers , 4 types, 48 molecules ![](data/chem/img/D3T.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-D3T / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2008 |
Radiation | Monochromator: sagitally focused Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 44203 / Num. obs: 44203 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 110.1 Å2 / Rsym value: 0.107 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4339 / Rsym value: 0.745 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HWT Resolution: 3→39.11 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 67836.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.1112 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→39.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: all.par / Topol file: all.top |