[English] 日本語
![](img/lk-miru.gif)
- PDB-5vzc: Post-catalytic complex of human Polymerase Mu (G433S) mutant with... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5vzc | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Post-catalytic complex of human Polymerase Mu (G433S) mutant with incoming dTTP | |||||||||||||||
![]() |
| |||||||||||||||
![]() | TRANSFERASE/DNA / Family X / nonhomologous end-joining / DNA double strand break repair / ribonucleotide incorporation / 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 | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 185.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 476.8 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5twpC ![]() 5twqC ![]() 5twrC ![]() 5twsC ![]() 5vz7C ![]() 5vz8C ![]() 5vz9C ![]() 5vzaC ![]() 5vzbC ![]() 5vzdC ![]() 5vzeC ![]() 5vzfC ![]() 5vzgC ![]() 5vzhC ![]() 5vziC ![]() 4m04S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39874.188 Da / Num. of mol.: 1 / Fragment: residues 134-494 / Mutation: G433S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-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) |
---|---|
#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 , 7 types, 452 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | #8: Chemical | ChemComp-TTP / | #9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.39 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 1.55→50 Å / Num. obs: 66859 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rpim(I) all: 0.034 / Rsym value: 0.083 / Χ2: 0.942 / Net I/σ(I): 23.64 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.29 / Num. unique obs: 3250 / CC1/2: 0.571 / Rpim(I) all: 0.379 / Rsym value: 0.605 / Χ2: 0.917 / % possible all: 97.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4M04 Resolution: 1.552→32.821 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 17.37 Details: THE AUTHORS STATE THAT THE ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT THE METAL OCCUPYING THE METAL A SITE (PEAK > 6 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ...Details: THE AUTHORS STATE THAT THE ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT THE METAL OCCUPYING THE METAL A SITE (PEAK > 6 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ADDED, SO THIS POSITION HAS BEEN PUTATIVELY MODELED AS SODIUM, WHICH IS CONSISTENT WITH ITS IDENTITY IN OTHER REPORTED STRUCTURES.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.552→32.821 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|