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- PDB-4dsk: Crystal structure of fragment DNA polymerase I from Bacillus stea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dsk | ||||||
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Title | Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, PPi and Calcium | ||||||
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![]() | TRANSFERASE/DNA / DNA polymerase / polymerization fidelity / pyrophosphorolysis / purine selectivity / blunt end extension / base stacking / DNA synthesis / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gan, J.H. / Abdur, R. / Liu, H.H. / Sheng, J. / Caton-Willians, J. / Soares, A.S. / Huang, Z. | ||||||
![]() | ![]() Title: Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase Authors: Gan, J.H. / Abdur, R. / Liu, H.H. / Sheng, J. / Caton-Willians, J. / Soares, A.S. / Huang, 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 | ![]() | 154.8 KB | Display | ![]() |
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PDB format | ![]() | 114.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.5 KB | Display | ![]() |
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Full document | ![]() | 466.3 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dsiC ![]() 4dsjC ![]() 4dslC ![]() 4dwiC ![]() 3ht3S S: Starting model for refinement C: citing same article ( |
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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 , 2 types, 2 molecules BC
#1: DNA chain | Mass: 4305.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized DNA |
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#2: DNA chain | Mass: 5163.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized DNA |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 66101.766 Da / Num. of mol.: 1 / Fragment: RESIDUES 298-876 / Mutation: A598D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DPO1 / Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: D9N168, UniProt: E1C9K5*PLUS, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 305 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-POP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate (pH 6.5), 18% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2011 / Details: mirrors |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→70.16 Å / Num. all: 45712 / Num. obs: 44295 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.085 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4497 / Rsym value: 0.374 / % possible all: 78.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HT3 Resolution: 2.18→70.16 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.453 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.076 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→70.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.236 Å / Total num. of bins used: 20
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