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- PDB-1d9f: CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d9f | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3' | ||||||
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![]() | TRANSFERASE/DNA / RNA / KLENOW FRAGMENT / 2'-O-AMINOPROPYL NUCLEOTIDES / RNA COMPLEX / TRANSFERASE-DNA | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Teplova, M. / Wallace, S.T. / Tereshko, V. / Minasov, G. / Simons, A.M. / Cook, P.D. / Manoharan, M. / Egli, M. | ||||||
![]() | ![]() Title: Structural origins of the exonuclease resistance of a zwitterionic RNA. Authors: Teplova, M. / Wallace, S.T. / Tereshko, V. / Minasov, G. / Symons, A.M. / Cook, P.D. / Manoharan, M. / Egli, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | 104.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.7 KB | Display | ![]() |
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Full document | ![]() | 481.8 KB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA/RNA hybrid | Mass: 1230.882 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: URACIL HAS 3-AMINOPROPYL BOUND TO O2* | ||
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#2: Protein | Mass: 68193.750 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: DPO1_ECOLI, UniProt: P00582*PLUS, DNA-directed DNA polymerase | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: SODIUM CITRATE, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: SODIUM CITRATE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 30, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99503 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→35 Å / Num. all: 20110 / Num. obs: 20110 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.23 % / Rmerge(I) obs: 0.078 |
Reflection | *PLUS Highest resolution: 3 Å |
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Processing
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Refinement | Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |