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Yorodumi- PDB-6p1n: Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p1n | ||||||
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Title | Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dAMPNPP | ||||||
Components |
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Keywords | TRANSFERASE / Family X polymerase / NHEJ | ||||||
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 / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kaminski, A.M. / Pedersen, L.C. / Bebenek, K. / Chiruvella, K.K. / Ramsden, D.A. / Kunkel, T.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine. Authors: Kaminski, A.M. / Chiruvella, K.K. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p1n.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p1n.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 6p1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p1n_validation.pdf.gz | 830.8 KB | Display | wwPDB validaton report |
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Full document | 6p1n_full_validation.pdf.gz | 832 KB | Display | |
Data in XML | 6p1n_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6p1n_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/6p1n ftp://data.pdbj.org/pub/pdb/validation_reports/p1/6p1n | HTTPS FTP |
-Related structure data
Related structure data | 6p1mC 6p1oC 6p1pC 6p1qC 6p1rC 6p1sC 6p1tC 6p1uC 6p1vC 6p1wC 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: 39844.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 (DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase |
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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 2772.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: DNA chain | Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 7 types, 392 molecules
#5: Chemical | ChemComp-DZ4 / | ||||||||||
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#6: Chemical | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-EPE / | #11: 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: 2.862 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 100mM NaCl, 10% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 6, 2015 / 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: 1.6→50 Å / Num. obs: 60668 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.059 / Rsym value: 0.057 / Χ2: 1.117 / Net I/σ(I): 96.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.1 % / Num. unique obs: 2842 / Rpim(I) all: 0.212 / Rrim(I) all: 0.403 / Rsym value: 0.339 / Χ2: 0.712 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M04 Resolution: 1.6→26.659 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→26.659 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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