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Yorodumi- PDB-6wid: Nucleotide incorporation intermediate into quaternary complex of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wid | |||||||||
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Title | Nucleotide incorporation intermediate into quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / Family X polymerase / nonhomologous end-joining / DNA double-strand break repair / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / 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: 1.5 Å | |||||||||
Authors | Kaminski, A.M. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break. Authors: Kaminski, A.M. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wid.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wid.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/6wid ftp://data.pdbj.org/pub/pdb/validation_reports/wi/6wid | HTTPS FTP |
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-Related structure data
Related structure data | 6wicC 6wieC 4m04S S: Starting model for refinement C: citing same article (ref.) |
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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: 40054.434 Da / Num. of mol.: 1 / Fragment: UNP residues 132-494 / Mutation: P398-P410 deletion replaced by G410 linker Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase |
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-DNA chain , 4 types, 4 molecules TUPD
#2: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 886.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 9 types, 360 molecules
#6: Chemical | ChemComp-DUP / | ||||||||||||
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#7: Chemical | ChemComp-PPV / | ||||||||||||
#8: Chemical | #9: Chemical | ChemComp-NA / | #10: Chemical | ChemComp-CL / | #11: Chemical | ChemComp-1PE / | #12: Chemical | #13: Chemical | ChemComp-PEG / | #14: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 40-45.5 mM MES, pH 5.6, 0.16-0.182 M potassium chloride, 8.2-9.1 mM magnesium sulfate, 8.2-9.1% w/v PEG400 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 71251 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 14.06 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.037 / Rrim(I) all: 0.091 / Rsym value: 0.083 / Χ2: 1.215 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 3524 / CC1/2: 0.848 / CC star: 0.958 / Rpim(I) all: 0.255 / Rrim(I) all: 0.606 / Rsym value: 0.548 / Χ2: 0.42 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4M04 Resolution: 1.5→31.02 Å / SU ML: 0.1371 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.8136
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→31.02 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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