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Open data
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Basic information
Entry | Database: PDB / ID: 2kfz | ||||||
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Title | KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND ZINC ONLY | ||||||
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![]() | TRANSFERASE/DNA / POLYMERASE (EXONUCLEASE)-DNA COMPLEX / ![]() | ||||||
Function / homology | ![]() 5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 145 KB | Display | ![]() |
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PDB format | ![]() | 109.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: 2130.460 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
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#2: Protein | Mass: 68193.750 Da / Num. of mol.: 1 / Fragment: LARGE FRAGMENT, KLENOW FRAGMENT / Mutation: V324M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | ![]() Nonpolymer details | ATOM O3* OF RESIDUE 1006B HAS BEEN REPLACED BY THE HETEROATOM | |
-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![]() | pH: 5.8 / Details: 1.4 M NA CITRATE PH 5.8 | |||||||||||||||
Components of the solutions | Name: SODIUM CITRATE | |||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6 / 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: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 2.03→20 Å / Num. obs: 59988 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.063 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.332 / % possible all: 97.6 |
Reflection | *PLUS Num. measured all: 422599 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS Rmerge(I) obs: 0.332 |
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Processing
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Refinement | Method to determine structure![]() Details: BULK-SOLVENT CORRECTION WAS USED TO EXTEND LOW-RES. LIMIT TO 20 ANGSTROMS ONLY LAST THREE NUCLEOTIDES OF NUCLEIC ACID COULD BE MODELED INTO ELECTRON DENSITY. ALTHOUGH MG2+ WAS SOAKED INTO ...Details: BULK-SOLVENT CORRECTION WAS USED TO EXTEND LOW-RES. LIMIT TO 20 ANGSTROMS ONLY LAST THREE NUCLEOTIDES OF NUCLEIC ACID COULD BE MODELED INTO ELECTRON DENSITY. ALTHOUGH MG2+ WAS SOAKED INTO THESE CRYSTALS, IT COULD NOT BE LOCATED AT THE ACTIVE SITE.
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.05 Å / Total num. of bins used: 30
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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