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- PDB-7u7t: Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u7t | ||||||||||||
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Title | Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 0.05 mM Mg2+ for 600s | ||||||||||||
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![]() | TRANSFERASE/DNA / Polymerase / TRANSFERASE / TRANSFERASE-DNA complex | ||||||||||||
Function / homology | ![]() response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chang, C. / Gao, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Authors: Chang, C. / Lee Luo, C. / Gao, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.4 KB | Display | ![]() |
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PDB format | ![]() | 94.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7u72C ![]() 7u73C ![]() 7u74C ![]() 7u75C ![]() 7u76C ![]() 7u77C ![]() 7u78C ![]() 7u79C ![]() 7u7aC ![]() 7u7bC ![]() 7u7cC ![]() 7u7dC ![]() 7u7eC ![]() 7u7fC ![]() 7u7gC ![]() 7u7iC ![]() 7u7jC ![]() 7u7kC ![]() 7u7lC ![]() 7u7rC ![]() 7u7sC ![]() 7u7uC ![]() 7u7vC ![]() 7u7wC ![]() 7u7xC ![]() 7u7yC ![]() 7u7zC ![]() 7u80C ![]() 7u81C ![]() 7u82C ![]() 7u83C ![]() 7u84C ![]() 4ecqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 48617.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 423 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/XG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/XG4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-XG4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% PEG 2000MME, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→42.71 Å / Num. obs: 64445 / % possible obs: 97.3 % / Redundancy: 5.564 % / Biso Wilson estimate: 21.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 0.89 / Net I/σ(I): 17.36 / Num. measured all: 694913 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ECQ Resolution: 1.55→42.71 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.14 / 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: 104.9 Å2 / Biso mean: 29.2178 Å2 / Biso min: 12.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→42.71 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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