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Open data
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Basic information
Entry | Database: PDB / ID: 2kzm | ||||||
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Title | KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE | ||||||
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![]() | TRANSFERASE/DNA / POLYMERASE / EXONUCLEASE / TWO METAL ION / NUCLEOTIDYLTRANSFERASE-DNA COMPLEX / TRANSFERASE-DNA complex | ||||||
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 | ![]() ![]() | ||||||
![]() | Brautigam, C.A. / Sun, S. / Piccirilli, J.A. / Steitz, T.A. | ||||||
![]() | ![]() Title: Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli. Authors: Brautigam, C.A. / Sun, S. / Piccirilli, J.A. / Steitz, T.A. #1: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.3 KB | Display | ![]() |
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PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 34.5 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 chain | Mass: 2402.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RANDOM SEQUENCE |
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#2: Protein | Mass: 68193.750 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, LARGE FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 64 % Description: STRUCTURE WAS SOLVED USING IN-HOUSE HIGH-RESOLUTION STRUCTURE | |||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.4 M SODIUM CITRATE PH 5.8, pH 5.5, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6 / 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: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Jun 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 23855 / % possible obs: 87.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.066 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.211 / % possible all: 73.9 |
Reflection | *PLUS Num. obs: 22445 / % possible obs: 89.1 % / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 73.9 % / Rmerge(I) obs: 0.211 |
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Processing
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Refinement | Method to determine structure: RIGID-BODY REFINEMENT / Resolution: 2.6→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 Details: BULK-SOLVENT CORRECTION WAS USED TO EXTEND LOW-RES LIMIT TO 20 ANGSTROMS. ONLY THE LAST TWO NUCLEOTIDES OF NUCLEIC ACID COULD BE MODELED INTO THE ELECTRON DENSITY.
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.63 Å / Total num. of bins used: 30
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.242 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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