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Yorodumi- PDB-1dpi: STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dpi | ||||||
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Title | STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP | ||||||
Components | DNA POLYMERASE I KLENOW FRAGMENT | ||||||
Keywords | NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information 5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / base-excision repair / DNA-templated DNA replication / double-strand break repair / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair ...5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / base-excision repair / DNA-templated DNA replication / double-strand break repair / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Beese, L. / Ollis, D. / Steitz, T. | ||||||
Citation | Journal: Nature / Year: 1985 Title: Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Authors: Ollis, D.L. / Brick, P. / Hamlin, R. / Xuong, N.G. / Steitz, T.A. #1: Journal: Nature / Year: 1985 Title: Domain of E. Coli DNA Polymerase I Showing Sequence Homology to T7 DNA Polymerase Authors: Ollis, D.L. / Kline, C. / Steitz, T.A. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Crystallization and 7 Angstroms Resolution Electron Density Map of the Large Fragment of Escherichia Coli DNA Polymerase I Authors: Brick, P. / Ollis, D. / Steitz, T.A. #3: Journal: J.Biol.Chem. / Year: 1982 Title: Nucleotide Sequence of the Escherichia Coli Pola Gene and Primary Structure of DNA Polymerase I Authors: Joyce, C.M. / Kelley, W.S. / Grindley, N.D.F. #4: Journal: J.Biol.Chem. / Year: 1982 Title: Escherichia Coli DNA Polymerase I. Sequence Characterization and Secondary Structure Prediction Authors: Brown, W.E. / Stump, K.H. / Kelley, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dpi.cif.gz | 31.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dpi.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dpi_validation.pdf.gz | 313.6 KB | Display | wwPDB validaton report |
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Full document | 1dpi_full_validation.pdf.gz | 313.6 KB | Display | |
Data in XML | 1dpi_validation.xml.gz | 830 B | Display | |
Data in CIF | 1dpi_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpi ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68161.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: T7 / Plasmid: T7 / Gene (production host): T7 / References: UniProt: P00582, DNA-directed DNA polymerase |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.07 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion / Details: Brick, P., (1983) J.Mol.Biol., 166, 453. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 20000 / Num. measured all: 80000 / Rmerge(I) obs: 0.05-0.006 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.2 / Highest resolution: 2.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refinement | *PLUS Rfactor obs: 0.2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |