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Yorodumi- PDB-1d9f: CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGM... -
+Open data
-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' | ||||||
Components |
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Keywords | TRANSFERASE/DNA / RNA / KLENOW FRAGMENT / 2'-O-AMINOPROPYL NUCLEOTIDES / RNA COMPLEX / TRANSFERASE-DNA | ||||||
Function / homology | Function and homology information 5'-3' exonuclease activity / 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 ...5'-3' exonuclease activity / 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 / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Teplova, M. / Wallace, S.T. / Tereshko, V. / Minasov, G. / Simons, A.M. / Cook, P.D. / Manoharan, M. / Egli, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d9f.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d9f.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d9f_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 1d9f_full_validation.pdf.gz | 481.8 KB | Display | |
Data in XML | 1d9f_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 1d9f_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d9f ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d9f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) Keywords: DNA TETRAMER, CARRYING 2'-O-AMINOPROPYL RNA MODIFICATION: 5'-D(TT)-AP(U)- D(T)- 3' 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99503 |
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 |
-Processing
Software |
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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 |