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Yorodumi- PDB-2gws: Crystal Structure of human DNA Polymerase lambda with a G/G misma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gws | ||||||
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Title | Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus | ||||||
Components |
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Keywords | Transferase/DNA / DNA polymerase lambda / family X / mismatch extension / mutagenesis / NHEJ / 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 / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Garcia-Diaz, M. / Picher, A.J. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A. / Blanco, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2006 Title: Promiscuous mismatch extension by human DNA polymerase lambda. Authors: Picher, A.J. / Garcia-Diaz, M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A. / Blanco, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gws.cif.gz | 327.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gws.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gws_validation.pdf.gz | 518.9 KB | Display | wwPDB validaton report |
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Full document | 2gws_full_validation.pdf.gz | 543 KB | Display | |
Data in XML | 2gws_validation.xml.gz | 59.2 KB | Display | |
Data in CIF | 2gws_validation.cif.gz | 86.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/2gws ftp://data.pdbj.org/pub/pdb/validation_reports/gw/2gws | HTTPS FTP |
-Related structure data
Related structure data | 1rztS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 | The asymmetric unit contains four biological units |
-Components
-DNA chain , 3 types, 12 molecules TFJNPGKRDHLQ
#1: DNA chain | Mass: 3344.188 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: DNA chain | Mass: 1865.240 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: DNA chain | Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Protein , 1 types, 4 molecules AEIM
#4: Protein | Mass: 37479.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 6 types, 814 molecules
#5: Chemical | ChemComp-NA / #6: Chemical | #7: Chemical | ChemComp-MG / | #8: Chemical | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.14 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 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: 2.4→50 Å / Num. obs: 76713 / % possible obs: 98.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.131 / Χ2: 1.078 / Net I/σ(I): 15.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1RZT Resolution: 2.4→50 Å / σ(F): 0
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Solvent computation | Bsol: 34.197 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 44.689 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Xplor file |
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