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Open data
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Basic information
Entry | Database: PDB / ID: 4f5q | ||||||
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Title | Closed ternary complex of R283K DNA polymerase beta | ||||||
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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 | ![]() ![]() | ||||||
![]() | Freudenthal, B.D. / Beard, W.A. / Wilson, S.H. | ||||||
![]() | ![]() Title: Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Authors: Freudenthal, B.D. / Beard, W.A. / Wilson, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.1 KB | Display | ![]() |
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PDB format | ![]() | 123.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4f5nC ![]() 4f5oC ![]() 4f5pC ![]() 4f5rC ![]() 2fmsS 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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Details | The biological assembly is a monomer in each asymetric unit. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 38213.656 Da / Num. of mol.: 1 / Mutation: R283K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P06746, ![]() ![]() |
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-DNA chain , 3 types, 3 molecules DPT
#2: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polydeoxyribonucleotide from IDT / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 112 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/6CF.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/6CF.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-6CF / | #7: Chemical | #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.33 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50mM Imidazole, 350mM Sodium Acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 2, 2011 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors VarimaxHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→28 Å / Num. all: 112322 / Num. obs: 112322 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 36.11 Å2 / Rmerge(I) obs: 0.098 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2FMS Resolution: 2.25→21.105 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 32.43 / 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 / Bsol: 46.565 Å2 / ksol: 0.413 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.25→21.105 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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