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Yorodumi- PDB-5vzf: Post-catalytic complex of human Polymerase Mu (W434A) mutant with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vzf | |||||||||||||||
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Title | Post-catalytic complex of human Polymerase Mu (W434A) mutant with incoming dTTP | |||||||||||||||
Components |
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Keywords | TRANSFERASE/DNA / Family X DNA polymerase / 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: 1.65 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 | 5vzf.cif.gz | 187.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vzf.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/5vzf ftp://data.pdbj.org/pub/pdb/validation_reports/vz/5vzf | HTTPS FTP |
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-Related structure data
Related structure data | 5twpC 5twqC 5twrC 5twsC 5vz7C 5vz8C 5vz9C 5vzaC 5vzbC 5vzcC 5vzdC 5vzeC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39729.027 Da / Num. of mol.: 1 / Fragment: UNP residues 134-494 Mutation: W434A, deletion of Pro398-Pro410 replaced by Gly410 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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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 413 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-EDO / | #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | Weak anomalous signal is observed at one position in this structure--at the metal occupying the ...Weak anomalous signal is observed at one position in this structure--at the metal occupying the HhH2 site (peak greater than 4.5 sigma). No known anomalous scatterers were added, so these positions have been putatively modeled as sodium, which is consistent with its identity in other reported structures |
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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: 2.85 Å3/Da / Density % sol: 56.8 % |
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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: 1.65→50 Å / Num. obs: 55355 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rpim(I) all: 0.027 / Rsym value: 0.066 / Χ2: 0.937 / Net I/σ(I): 26.33 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.71 / Num. unique obs: 2725 / CC1/2: 0.816 / Rpim(I) all: 0.299 / Rsym value: 0.694 / Χ2: 0.817 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M04 Resolution: 1.65→32.79 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 17.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→32.79 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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