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Yorodumi- PDB-1ksp: DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ksp | ||||||
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Title | DNA polymerase I Klenow fragment (E.C.2.7.7.7) mutant/DNA complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / EXONUCLEASE / PHOSPHOROTHIOATE / TRANSFERASE-DNA COMPLEX | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT / Resolution: 2.3 Å | ||||||
Authors | Brautigam, C.A. / Steitz, T.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. Authors: Brautigam, C.A. / Steitz, T.A. #1: Journal: Embo J. / Year: 1991 Title: Structural Basis for the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism Authors: Beese, L.S. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ksp.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ksp.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ksp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ksp_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 1ksp_full_validation.pdf.gz | 454.8 KB | Display | |
Data in XML | 1ksp_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 1ksp_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ksp ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ksp | 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 chain | Mass: 883.687 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Protein | Mass: 68193.750 Da / Num. of mol.: 1 / Mutation: V324M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCJ155 / Production host: Escherichia coli (E. coli) / Strain (production host): CJ 376 / Keywords: MUTATION: V324M / References: UniProt: P00582, DNA-directed DNA polymerase | ||
#3: Chemical | #4: 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: 3.3 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: 1.4 M NA CITRATE PH 5.8 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Brick, P., (1983) J. Mol. Biol., 166, 453. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 200444 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Rsym value: 0.064 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.407 / % possible all: 96.3 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 31495 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Num. measured all: 200444 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID-BODY REFINEMENT Starting model: IN-HOUSE HIGH-RESOLUTION STRUCTURE Resolution: 2.3→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 Details: ONLY THE THREE 3'-TERMINAL BASES OF THE DNA COULD BE MODELED INTO ELECTRON DENSITY. ONLY THE LAST PHOSPHATE IS MODIFIED.
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Displacement parameters | Biso mean: 38.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.33 Å / Total num. of bins used: 30
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.3301 / Rfactor Rwork: 0.2977 |