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Yorodumi- PDB-4dfm: Crystal structure of the large fragment of DNA polymerase I from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dfm | ||||||
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Title | Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA Polymerase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleoside binding / 5'-3' exonuclease activity / 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 / Difference Fourier Techniques / Resolution: 1.886 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 | 4dfm.cif.gz | 252.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dfm.ent.gz | 197.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dfm_validation.pdf.gz | 833.7 KB | Display | wwPDB validaton report |
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Full document | 4dfm_full_validation.pdf.gz | 840.7 KB | Display | |
Data in XML | 4dfm_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 4dfm_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/4dfm ftp://data.pdbj.org/pub/pdb/validation_reports/df/4dfm | HTTPS FTP |
-Related structure data
Related structure data | 4df4C 4df8C 4dfjC 4dfkC 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: 3657.395 Da / Num. of mol.: 1 / Fragment: DNA Primer / Source method: obtained synthetically / Details: DNA synthesizer |
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#3: DNA chain | Mass: 4924.192 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Details: DNA synthesizer |
-Non-polymers , 5 types, 259 molecules
#4: Chemical | ChemComp-0L6 / | ||||||
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#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-FMT / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 8000, 200mM Mg-Formate, 100 mM Tris 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: X06DA / Wavelength: 0.99987 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2011 |
Radiation | Monochromator: Bartels Monochromator, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.886→47.15 Å / Num. all: 49434 / Num. obs: 48761 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 12.77 |
Reflection shell | Resolution: 1.89→1.94 Å / Mean I/σ(I) obs: 1.83 / Num. unique all: 3643 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier Techniques Starting model: PDB ENTRY 3M8S Resolution: 1.886→46.878 Å / SU ML: 0.23 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.5 / 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: 37.218 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.653 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.886→46.878 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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