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Yorodumi- PDB-4elv: Snapshot of the large fragment of DNA polymerase I from Thermus A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4elv | ||||||
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Title | Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / modified nucleotides / A family / DNA synthesis / rigid linker / elongation of modified DNA / non-natural nucleotide / 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) synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Marx, A. / Diederichs, K. / Obeid, S. | ||||||
Citation | Journal: To be Published Title: Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines Authors: Obeid, S. / Bu kamp, H. / 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 | 4elv.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4elv.ent.gz | 203.4 KB | Display | PDB format |
PDBx/mmJSON format | 4elv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/4elv ftp://data.pdbj.org/pub/pdb/validation_reports/el/4elv | HTTPS FTP |
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-Related structure data
Related structure data | 3ojsS S: Starting model for refinement |
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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: UNP RESIDUES 293-832 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3741.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer / Source: (synth.) synthetic (others) |
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#3: DNA chain | Mass: 4964.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer / Source: (synth.) synthetic (others) |
-Non-polymers , 7 types, 335 molecules
#4: Chemical | #5: Chemical | ChemComp-0R7 / [[( | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PGE / | #8: Chemical | #9: Chemical | ChemComp-CA / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 50 mM Tris HCl pH=8.4, 0.2 M NH4Cl, 10 mM CaCl2, 34% PEG 4000, 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: Aug 13, 2010 Details: Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator |
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: 1.89→50 Å / Num. all: 50305 / Num. obs: 50305 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.118 |
Reflection shell | Resolution: 1.89→2 Å / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 1.2 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OJS Resolution: 1.9→47.291 Å / SU ML: 0.2 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 21.52 / 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: 42.089 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→47.291 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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