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Yorodumi- PDB-5vzb: Post-catalytic complex of human Polymerase Mu (G433S) mutant with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vzb | |||||||||||||||
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Title | Post-catalytic complex of human Polymerase Mu (G433S) mutant with incoming UTP | |||||||||||||||
Components |
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Keywords | TRANSFERASE/DNA / Family X / nonhomologous end-joining / DNA double strand break repair / ribonucleotide incorporation / 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 | Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu. Authors: Moon, A.F. / Pryor, J.M. / 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 | 5vzb.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vzb.ent.gz | 140 KB | Display | PDB format |
PDBx/mmJSON format | 5vzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/5vzb ftp://data.pdbj.org/pub/pdb/validation_reports/vz/5vzb | HTTPS FTP |
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-Related structure data
Related structure data | 5twpC 5twqC 5twrC 5twsC 5vz7C 5vz8C 5vz9C 5vzaC 5vzcC 5vzdC 5vzeC 5vzfC 5vzgC 5vzhC 5vziC 4m04S 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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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules TD
#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / DNA/RNA hybrid , 2 types, 2 molecules AP
#1: Protein | Mass: 39874.188 Da / Num. of mol.: 1 / Fragment: residues 134-494 / Mutation: G433S 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) / References: UniProt: Q9NP87, DNA-directed DNA polymerase |
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#3: DNA/RNA hybrid | Mass: 1496.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 387 molecules
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | #8: Chemical | ChemComp-UTP / | #9: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 90mM HEPES pH 7.5, 18% PEG4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2017 / Details: Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing 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: 72904 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rpim(I) all: 0.027 / Rsym value: 0.065 / Χ2: 0.933 / Net I/σ(I): 25.34 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.45 / Num. unique obs: 3437 / CC1/2: 0.688 / Rpim(I) all: 0.339 / Rsym value: 0.578 / Χ2: 0.836 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M04 Resolution: 1.5→32.328 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 17.2 Details: THE AUTHORS STATE THAT THE ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT THE METAL OCCUPYING THE HHH2 SITE (PEAK > 10 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ADDED, ...Details: THE AUTHORS STATE THAT THE ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT THE METAL OCCUPYING THE HHH2 SITE (PEAK > 10 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ADDED, SO THIS POSITION HAS BEEN PUTATIVELY MODELED AS SODIUM, WHICH IS CONSISTENT WITH ITS IDENTITY IN OTHER REPORTED STRUCTURES.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→32.328 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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