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Yorodumi- PDB-3oju: Snapshot of the large fragment of DNA polymerase I from Thermus A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oju | ||||||
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Title | Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing c5 modified thymidies | ||||||
Components |
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Keywords | Transferase/DNA / DNA polymerase / C5 modified nucleotide analogs / binding pocket / spin-labeled triphosphate / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Marx, A. / Diederichs, K. / Obeid, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Authors: Obeid, 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 | 3oju.cif.gz | 362 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oju.ent.gz | 295.8 KB | Display | PDB format |
PDBx/mmJSON format | 3oju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/3oju ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3oju | HTTPS FTP |
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-Related structure data
Related structure data | 3ojsC 3m8rS C: citing same article (ref.) 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 292-832 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Plasmid: pET-21b / 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 / Source method: obtained synthetically / Details: DNA PRIMER |
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#3: DNA chain | Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA TEMPLATE |
-Non-polymers , 5 types, 215 molecules
#4: Chemical | ChemComp-SSJ / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PGE / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.05M Tris HCl ph 9, 0.2M NH4Cl, 0.01M CaCl2, 26% 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: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009 Details: vertically collimating mirror (M1, focus at infinity), followed by Bartels Monochromator with dual channel cut crystals |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals 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: 1.99→50 Å / Num. obs: 32113 / % possible obs: 74.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 39.017 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.66 |
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.84 / % possible all: 28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3M8R Resolution: 2→47.208 Å / SU ML: 0.25 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.99 / 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: 53.651 Å2 / ksol: 0.439 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.208 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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