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Open data
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Basic information
Entry | Database: PDB / ID: 4m04 | ||||||
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Title | Human DNA Polymerase Mu ternary complex | ||||||
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![]() | TRANSFERASE/DNA / polymerase / DNA break repair / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | ||||||
![]() | ![]() Title: Sustained active site rigidity during synthesis by human DNA 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.9 KB | Display | ![]() |
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Full document | ![]() | 789.8 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lzdC ![]() 4lzgC ![]() 4m0aC ![]() 2ihmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Fragment: Polymerase Mu Loop2 deletion variant, UNP residues 132-494 Source method: isolated from a genetically manipulated source Details: Modified version of the pGEX4T3 vector backbone, where a TEV protease cleavage site has been inserted downstream of the thrombin cleavage site, and the sequence of the multicloning site has ...Details: Modified version of the pGEX4T3 vector backbone, where a TEV protease cleavage site has been inserted downstream of the thrombin cleavage site, and the sequence of the multicloning site has been replaced by that from the pMALX vector (Moon et al, 2010). Three TGA stop codons have been inserted downstream of the MCS, each utilizing a different reading frame. Source: (gene. exp.) ![]() ![]() ![]() |
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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 / Details: synthesized by Oligos Etc |
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#3: DNA chain | Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by Oligos Etc |
#4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by Oligos Etc |
-Non-polymers , 7 types, 390 molecules ![](data/chem/img/DUP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-DUP / | ||||||||||
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#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-NA / | #10: Chemical | ChemComp-EPE / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystals were grown by mixing 1uL of protein/DNA mixture with 1uL mother liquor (85-90mM HEPES pH 7.5, 17-18% PEG4000), using the sitting drop vapor diffusion technique. Crystals were then ...Details: Crystals were grown by mixing 1uL of protein/DNA mixture with 1uL mother liquor (85-90mM HEPES pH 7.5, 17-18% PEG4000), using the sitting drop vapor diffusion technique. Crystals were then transferred to a cryoprotectant solution containing 0.1M HEPES pH 7.5, 10mM MgCl2, 50mM NaCl, 20% PEG4000, 5% glycerol, 1mM dUMPNPP in two steps. , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 8, 2012 / Details: VariMaxHF mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.898→50 Å / Num. all: 36290 / Num. obs: 36290 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 24.04 Å2 / Rsym value: 0.064 / Χ2: 1.023 / Net I/σ(I): 13.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IHM (molecule B) Resolution: 1.898→23.174 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8651 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.43 Å2 / Biso mean: 15.4651 Å2 / Biso min: 1.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.898→23.174 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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