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- PDB-4dwi: 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: 4dwi | ||||||
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Title | Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self complementary DNA, Se-dGTP 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 | ![]() | 150.7 KB | Display | ![]() |
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PDB format | ![]() | 112.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.6 KB | Display | ![]() |
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Full document | ![]() | 492.2 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dsiC ![]() 4dsjC ![]() 4dskC ![]() 4dslC ![]() 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
-Protein / DNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 66245.898 Da / Num. of mol.: 1 / 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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#2: DNA chain | Mass: 3029.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized DNA |
-Non-polymers , 5 types, 221 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/9MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/9MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-9MG / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0. M Bis-Tris, pH 6.5, 2.0 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2011 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→70.01 Å / Num. all: 75057 / Num. obs: 72655 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.099 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 7408 / Rsym value: 0.383 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 3HT3 Resolution: 1.85→70.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.132 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.139 / 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: 25.043 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→70.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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