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Yorodumi- PDB-4dfj: Crystal structure of the large fragment of DNA Polymerase I from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dfj | ||||||
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Title | Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dTTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA Polymerase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleoside binding / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Bergen, K. / Steck, A. / Struett, S. / Baccaro, A. / Welte, W. / Diederichs, K. / Marx, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates. Authors: Bergen, K. / Steck, A.L. / Strutt, S. / Baccaro, A. / Welte, W. / Diederichs, K. / Marx, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dfj.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dfj.ent.gz | 201.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/4dfj ftp://data.pdbj.org/pub/pdb/validation_reports/df/4dfj | HTTPS FTP |
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-Related structure data
Related structure data | 4df4C 4df8C 4dfkC 4dfmC 4dfpC 3m8sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: Pol I, pol1, polA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P19821, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3617.371 Da / Num. of mol.: 1 / Fragment: DNA Primer / Source method: obtained synthetically / Details: DNA synthesizer |
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#3: DNA chain | Mass: 4948.217 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Details: DNA synthesizer |
-Non-polymers , 6 types, 258 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-0KL / | #6: Chemical | ChemComp-FMT / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2011 |
Radiation | Monochromator: LN2 cooled fixed exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 46509 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 16.71 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 3M8S Resolution: 1.9→41.807 Å / SU ML: 0.17 / Isotropic thermal model: isotropic and tls / σ(F): 2.02 / Phase error: 20.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.762 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.807 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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