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- PDB-3lwm: Structure of the large fragment of thermus aquaticus DNA polymera... -
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Basic information
Entry | Database: PDB / ID: 3lwm | ||||||
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Title | Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP | ||||||
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![]() | TRANSFERASE/DNA / DNA replication / DNA polymerases / DNA-binding / DNA-directed DNA polymerase / amino acid-templating mechanism / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex / blunt-ended DNA / template-independent DNA synthesis / terminal deoxynucleotidyl transferase / template-independent nucleotide addition | ||||||
Function / homology | ![]() nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marx, A. / Diederichs, K. / Obeid, S. | ||||||
![]() | ![]() Title: Replication through an abasic DNA lesion: structural basis for adenine selectivity Authors: Obeid, S. / Blatter, N. / Kranaster, R. / Schnur, A. / Diederichs, K. / Welte, W. / Marx, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.8 KB | Display | ![]() |
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PDB format | ![]() | 208.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810 KB | Display | ![]() |
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Full document | ![]() | 821.6 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lwlC ![]() 3ktqS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, UNP residues 293-832 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3641.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA |
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#3: DNA chain | Mass: 3670.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA |
-Non-polymers , 6 types, 169 molecules ![](data/chem/img/DDS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DDS / | ||||||||
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#5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-NA / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.05M TRIS HCl, pH 8, 0.2M ammonium chloride, 0.01M calcium chloride and 35% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2009 Details: vertically collimating mirror (M1, focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry, and a toroidal mirror (M2) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.186→50 Å / Num. obs: 32557 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.61 % / Biso Wilson estimate: 42.37 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.96 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 8.08 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.53 / Num. unique all: 4863 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3KTQ Resolution: 2.186→47.455 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.843 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 22.85 / 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: 44.855 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.08 Å2 / Biso mean: 52.4 Å2 / Biso min: 14.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.186→47.455 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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