+Open data
-Basic information
Entry | Database: PDB / ID: 6ipk | ||||||
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Title | Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP | ||||||
Components | DNA-directed DNA/RNA polymerase mu | ||||||
Keywords | TRANSFERASE / DNA Polymerase Mu / DNA break repair / Transferase-dNTP complex / 8-oxo-dGTP | ||||||
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: 2.15 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 | 6ipk.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipk.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 6ipk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ipk_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6ipk_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ipk_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6ipk_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipk ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipk | HTTPS FTP |
-Related structure data
Related structure data | 5zlcC 6aecC 6aehC 6ak5C 6ak6C 6ak8C 6ak9C 6akhC 6ipdC 6ipeC 6ipfC 6ipgC 6iphC 6ipiC 6ipjC 6iplC 6ipmC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 104 molecules
#2: Chemical | #3: Chemical | ChemComp-8DG / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EPE / | #6: 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: 2.35 Å3/Da / Density % sol: 47.6 % |
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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: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 21351 / % possible obs: 99.9 % / Redundancy: 13.32 % / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.15→2.28 Å / Redundancy: 13.88 % / Mean I/σ(I) obs: 5.78 / Num. unique obs: 3375 / CC1/2: 0.979 / Rrim(I) all: 0.364 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.017 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.206 / 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: 54.307 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→30 Å
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Refine LS restraints |
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