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- PDB-7l69: Crystal structure of human polymerase eta complexed with syn N7-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l69 | ||||||
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Title | Crystal structure of human polymerase eta complexed with syn N7-benzylguanine | ||||||
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![]() | REPLICATION / DPO4 / Y-family DNA polymerase / Translesion synthesis / TRANSFERASE / extension / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jung, H. / Lee, S. | ||||||
![]() | ![]() Title: Crystal structure of human polymerase eta complexed with syn N7-benzylguanine Authors: Jung, H. / Lee, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.7 KB | Display | ![]() |
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PDB format | ![]() | 83.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4o3nS S: Starting model for refinement |
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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
#1: Protein | Mass: 48325.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3691.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: DNA chain | Mass: 2506.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES pH 6.5 20% PEG2000 MME 5 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 35888 / % possible obs: 99.9 % / Redundancy: 11 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.151 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.91→1.94 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1774 / CC1/2: 0.699 / Rpim(I) all: 0.473 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4O3N Resolution: 1.91→49.5 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 35.31 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→49.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.95 Å
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