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- PDB-4rno: Crystal structure of human polymerase eta extending an abasic sit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rno | ||||||
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Title | Crystal structure of human polymerase eta extending an abasic site-dA pair by inserting dCTP opposite template G | ||||||
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![]() | TRANSFERASE/DNA / Protein / DNA / DNA Damage DNA-Directed DNA Polymerase / Adenosine Triphosphate / Y-family polymerase / trans-lesion synthesis (TLS) / DNA Binding / Abasic Site lesion bypass / TRANSFERASE-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 / regulation of DNA repair / error-prone translesion synthesis / 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 / regulation of DNA repair / error-prone translesion synthesis / 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 | ![]() ![]() ![]() | ||||||
![]() | Patra, A. / Egli, M. | ||||||
![]() | ![]() Title: Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase eta. Authors: Patra, A. / Zhang, Q. / Lei, L. / Su, Y. / Egli, M. / Guengerich, F.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.7 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766.6 KB | Display | ![]() |
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Full document | ![]() | 773.3 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rnmC ![]() 4rnnC ![]() 4o3nS C: citing same article ( 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: UNP residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Nucleic acids ... , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3529.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2435.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 59 molecules ![](data/chem/img/DCP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DCP / |
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#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M MES pH 5.5, 5mM magnesium chloride, 28% PEG 2000 MME , VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.82→50 Å / Num. obs: 10375 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.207 / Rsym value: 0.207 / Net I/σ(I): 5.025 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1810) / Classification: refinement | ||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4O3N Resolution: 2.82→42.776 Å / SU ML: 0.65 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 39.29 / 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 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→42.776 Å
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Refine LS restraints |
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LS refinement shell |
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