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- PDB-6ur9: DNA polymerase I Large Fragment from Bacillus stearothermophilus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ur9 | ||||||
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Title | DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+ | ||||||
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![]() | REPLICATION/DNA / DNA polymerase / 3'-amino-dGTP / Calcium / REPLICATION-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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, W. / Lelyveld, V.S. / Szostak, J.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase. Authors: Lelyveld, V.S. / Zhang, W. / Szostak, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.6 KB | Display | ![]() |
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PDB format | ![]() | 214.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 871.9 KB | Display | ![]() |
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Full document | ![]() | 883.6 KB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 63.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ur2C ![]() 6ur4C ![]() 6us5C ![]() 1l5uS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 66073.750 Da / Num. of mol.: 2 / Mutation: D598A/F710Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DPO1, polA / Production host: ![]() ![]() |
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-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 2724.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3936.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 358 molecules ![](data/chem/img/NG3.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NG3 / | ||
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#5: Chemical | ChemComp-CA / | ||
#6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.1 M MES, pH 5.4, 2M ammonium sulfate, 10 mM CaCl2, 2.5 % MPD, crystal soaked with 10 mM CaCl2 pH 8.8 buffer for 20 min |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Sep 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 89397 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Χ2: 0.96 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.55 / Num. unique obs: 8849 / CC1/2: 0.919 / Rpim(I) all: 0.184 / Rrim(I) all: 0.497 / Χ2: 0.573 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1L5U Resolution: 2.1→46.81 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.15 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.32 Å2 / Biso mean: 42.3488 Å2 / Biso min: 15.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→46.81 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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