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Yorodumi- PDB-5cp2: Human DNA polymerase lambda L431A mutant- Apoenzyme and complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cp2 | ||||||
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Title | Human DNA polymerase lambda L431A mutant- Apoenzyme and complex with 6 paired DNA | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase lambda / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Liu, M.S. / Tsai, M.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda Authors: Liu, M.S. / Tsai, H.Y. / Liu, X.X. / Ho, M.C. / Wu, W.J. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cp2.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cp2.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/5cp2 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/5cp2 | HTTPS FTP |
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-Related structure data
Related structure data | 4xq8C 4xrhC 5ca7C 5cb1C 5chgC 5cj7C 5cr0C 5cwrC 5ddmC 5ddyC 5dkwC 1xslS C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37306.477 Da / Num. of mol.: 2 / Fragment: UNP residues 242-575 / Mutation: L431A 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 #2: DNA chain | | Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-SO4 / | #5: 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: 2.57 Å3/Da / Density % sol: 52.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 30, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→30 Å / Num. obs: 35440 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 43.27 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XSL Resolution: 2.36→25.95 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→25.95 Å
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Refine LS restraints |
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LS refinement shell |
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