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Yorodumi- PDB-3hw8: ternary complex of DNA polymerase lambda of a two nucleotide gapp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hw8 | ||||||
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Title | ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site | ||||||
Components |
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Keywords | TRANSFERASE/DNA / scrunch site / X-family / polymerase / 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 | Function and homology information 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 / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
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. | ||||||
Citation | Journal: To be Published Title: Scrunching Durning 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hw8.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hw8.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hw8 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hw8 | HTTPS FTP |
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-Related structure data
Related structure data | 1xsnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37447.688 Da / Num. of mol.: 1 / Fragment: UNP residues 242-575, 39 kDa catalytic domain / Mutation: C543A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: PET22-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 3 types, 3 molecules BCD
#2: DNA chain | Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template strand |
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#3: DNA chain | Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer strand |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: downstream primer strand |
-Non-polymers , 5 types, 338 molecules
#5: Chemical | ChemComp-MG / | ||||||
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#6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-D3T / | #8: Chemical | ChemComp-EDO / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Dec 5, 2008 / Details: VariMax HF |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 38282 / Num. obs: 38282 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.092 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3479 / Rsym value: 0.522 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XSN Resolution: 1.95→24.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 602839.15 / 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: 49.8831 Å2 / ksol: 0.360105 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→24.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: all.par / Topol file: all.top |