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Yorodumi- PDB-5vz8: Post-catalytic complex of human Polymerase Mu (G433A) mutant with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vz8 | |||||||||||||||
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Title | Post-catalytic complex of human Polymerase Mu (G433A) 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 / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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 | 5vz8.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vz8.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vz8_validation.pdf.gz | 801.2 KB | Display | wwPDB validaton report |
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Full document | 5vz8_full_validation.pdf.gz | 801.1 KB | Display | |
Data in XML | 5vz8_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5vz8_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/5vz8 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/5vz8 | HTTPS FTP |
-Related structure data
Related structure data | 5twpC 5twqC 5twrC 5twsC 5vz7C 5vz9C 5vzaC 5vzbC 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: 39858.188 Da / Num. of mol.: 1 / Fragment: residues 134-494 / Mutation: G433A 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, 363 molecules
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-UTP / | #8: Chemical | #9: Chemical | ChemComp-EPE / | #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: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50mM HEPES pH 7.5, 10% 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: 1.6→50 Å / Num. obs: 59923 / % possible obs: 98.7 % / Redundancy: 7.2 % / Rpim(I) all: 0.03 / Rsym value: 0.076 / Χ2: 0.915 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2914 / CC1/2: 0.769 / Rpim(I) all: 0.344 / Rsym value: 0.752 / Χ2: 0.772 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M04 Resolution: 1.601→29.91 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 17.77 Details: THE AUTHORS STATE THAT ANOMALOUS SIGNAL IS OBSERVED AT TWO POSITIONS IN THIS STRUCTURE--AT THE METAL OCCUPYING THE HHH2 SITE (PEAK > 10 SIGMA), AND AT THE METAL OCCUPYING THE METAL A SITE ...Details: THE AUTHORS STATE THAT ANOMALOUS SIGNAL IS OBSERVED AT TWO POSITIONS IN THIS STRUCTURE--AT THE METAL OCCUPYING THE HHH2 SITE (PEAK > 10 SIGMA), AND AT THE METAL OCCUPYING THE METAL A SITE (PEAK > 6 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ADDED, SO THESE POSITIONS HAVE BEEN PUTATIVELY MODELED AS SODIUM (IN THE HHH2 SITE) AND MAGNESIUM (IN THE METAL A SITE), WHICH ARE CONSISTENT WITH THEIR IDENTITIES 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: 1.601→29.91 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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