+Open data
-Basic information
Entry | Database: PDB / ID: 5ddy | ||||||
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Title | Binary complex of human Polymerase lambda with dCTP | ||||||
Components | DNA polymerase lambda | ||||||
Keywords | TRANSFERASE / Polymerase lambda | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å | ||||||
Authors | Liu, M.S. / Tsai, M.D. | ||||||
Funding support | Taiwan, 1items
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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 | 5ddy.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ddy.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ddy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/5ddy ftp://data.pdbj.org/pub/pdb/validation_reports/dd/5ddy | HTTPS FTP |
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-Related structure data
Related structure data | 4xq8C 4xrhC 5ca7C 5cb1C 5chgC 5cj7C 5cp2C 5cr0C 5cwrC 5ddmC 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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Unit cell |
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-Components
#1: Protein | Mass: 37479.750 Da / Num. of mol.: 4 / Fragment: UNP residues 242-575 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: Chemical | ChemComp-MG / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-DCP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 3.0M Sodium Chloride |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.36→30 Å / Num. obs: 35439 / % possible obs: 99.8 % / Redundancy: 11 % / Biso Wilson estimate: 119.31 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1 / Net I/av σ(I): 26.277 / Net I/σ(I): 16.3 / Num. measured all: 390025 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Χ2: 1 / Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XSL Resolution: 3.36→29.658 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.26 / 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: 3.36→29.658 Å
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Refine LS restraints |
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LS refinement shell |
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