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- PDB-6vkp: Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vkp | ||||||
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Title | Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG | ||||||
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![]() | TRANSFERASE/DNA / DPO4 / Y-family DNA polymerase / Translesion synthesis / TRANSFERASE / extension / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jung, H. / Lee, S. | ||||||
![]() | ![]() Title: Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4. 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 | ![]() | 190.5 KB | Display | ![]() |
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PDB format | ![]() | 143.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jx4S 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
-DNA chain , 2 types, 4 molecules PBTC
#1: DNA chain | Mass: 4409.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: DNA chain | Mass: 5706.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Protein , 1 types, 2 molecules AD
#3: Protein | Mass: 39019.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dbh, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SULH_01230, SULI_01230, SULM_01230, SULN_01230, SULO_01240, SULZ_01250 Production host: ![]() ![]() References: UniProt: A0A0E3K6E9, UniProt: Q97W02*PLUS, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 71 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/DZ4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DZ4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | #6: 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: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM Tris 7.5 18% PEG 3350 100 mM magnesium acetate |
-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: Jul 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. obs: 35565 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rpim(I) all: 0.064 / Net I/σ(I): 15.68 |
Reflection shell | Resolution: 2.53→2.57 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1729 / CC1/2: 0.478 / Rpim(I) all: 0.637 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JX4 Resolution: 2.54→49.55 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 62.78 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→49.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.6 Å
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