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- PDB-5vs1: Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vs1 | |||||||||
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Title | Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in non-planar conformation | |||||||||
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Function / homology | ![]() Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Reed, A.J. / Suo, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta. Authors: Reed, A.J. / Suo, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vrwC ![]() 5vrxC ![]() 5vryC ![]() 5vrzC ![]() 5vs0C ![]() 5vs2C ![]() 5vs3C ![]() 5vs4C ![]() 4rpxS 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
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4909.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#4: Protein | ![]() Mass: 39070.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P06746, ![]() ![]() |
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-Non-polymers , 4 types, 57 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-TTP / | ![]() #7: Chemical | ChemComp-PEG / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350 PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 17, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→52.91 Å / Num. obs: 27883 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 1.976 % / Biso Wilson estimate: 45.504 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.071 / Χ2: 0.948 / Net I/σ(I): 12.96 / Num. measured all: 55105 / Scaling rejects: 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4rpx Resolution: 2.5→52.91 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.858 / SU B: 11.661 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.293 / ESU R Free: 0.341 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.22 Å2 / Biso mean: 38.657 Å2 / Biso min: 16.75 Å2
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Refinement step | Cycle: final / Resolution: 2.5→52.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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