+Open data
-Basic information
Entry | Database: PDB / ID: 6ipm | ||||||
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Title | Binary Complex of Human DNA Polymerase Mu with MgdCTP | ||||||
Components | DNA-directed DNA/RNA polymerase mu | ||||||
Keywords | TRANSFERASE / DNA Polymerase Mu / DNA break repair / Transferase-dNTP 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Chang, Y.K. / Wu, W.J. / Tsai, M.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. Authors: Chang, Y.K. / Huang, Y.P. / Liu, X.X. / Ko, T.P. / Bessho, Y. / Kawano, Y. / Maestre-Reyna, M. / Wu, W.J. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ipm.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipm.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ipm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ipm_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6ipm_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6ipm_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6ipm_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipm ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipm | HTTPS FTP |
-Related structure data
Related structure data | 5zlcC 6aecC 6aehC 6ak5C 6ak6C 6ak8C 6ak9C 6akhC 6ipdC 6ipeC 6ipfC 6ipgC 6iphC 6ipiC 6ipjC 6ipkC 6iplC 6ipnC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40054.434 Da / Num. of mol.: 1 / Mutation: deletions 398-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP87, DNA-directed DNA polymerase | ||
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#2: Chemical | ChemComp-DCP / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-SO4 / #5: 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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: May 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→30 Å / Num. obs: 42885 / % possible obs: 99.9 % / Redundancy: 13.9 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.068 / Net I/σ(I): 42.64 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4225 / Rpim(I) all: 0.222 / Rrim(I) all: 0.762 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.577 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.806 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→30 Å
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Refine LS restraints |
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