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- PDB-4u6p: Structural mechanism of error-free bypass of major benzo[a]pyrene... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u6p | ||||||
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Title | Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human polymerase kappa | ||||||
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![]() | TRANSFERASE/DNA / benzo[a]pyrene-N2-Guanine / DNA replication / DNA damage tolerance / polymerase kappa / Environment pollution / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV ...nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() unidentified (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jha, V.K. / Ling, H. | ||||||
![]() | ![]() Title: Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa. Authors: Jha, V. / Bian, C. / Xing, G. / Ling, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.2 KB | Display | ![]() |
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PDB format | ![]() | 163.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u7cC ![]() 2oh2S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60184.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 4 molecules CPDT
#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #3: DNA chain | Mass: 3982.596 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
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-Non-polymers , 4 types, 112 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: PEG 400 and potassium acetate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→46.233 Å / Num. obs: 50663 / % possible obs: 96.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.48→2.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.2 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OH2 Resolution: 2.593→46.233 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.71 / 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: 2.593→46.233 Å
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Refine LS restraints |
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LS refinement shell |
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