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- PDB-1k3w: Crystal structure of a trapped reaction intermediate of the DNA R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k3w | ||||||
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Title | Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Golan, G. / Zharkov, D.O. / Gilboa, R. / Fernandes, A.S. / Kycia, J.H. / Gerchman, S.E. / Rieger, R.A. / Grollman, A.P. / Shoham, G. | ||||||
![]() | ![]() Title: Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. Authors: Zharkov, D.O. / Golan, G. / Gilboa, R. / Fernandes, A.S. / Gerchman, S.E. / Kycia, J.H. / Rieger, R.A. / Grollman, A.P. / Shoham, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.2 KB | Display | ![]() |
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PDB format | ![]() | 119.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.5 KB | Display | ![]() |
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Full document | ![]() | 413.4 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 15.9 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 on special symmetry positions |
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Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3863.531 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 29814.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P50465, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-Non-polymers , 3 types, 401 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 60.79 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M Ammonium-sulfate, 0.1M sodium-citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion / PH range low: 5 / PH range high: 4.6 | |||||||||||||||||||||||||||||||||||||||||||||||||
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 QUANTUM 4 / Detector: CCD / Date: Feb 26, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→40 Å / Num. obs: 86586 / % possible obs: 95.2 % / Redundancy: 5.5 % / Rsym value: 0.083 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 2 % / Num. unique all: 3191 / Rsym value: 0.375 / % possible all: 71.4 |
Reflection | *PLUS Num. measured all: 471081 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 71.4 % / Rmerge(I) obs: 0.375 |
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Processing
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Refinement | Starting model: initial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION Resolution: 1.42→10 Å / Num. parameters: 25384 / Num. restraintsaints: 31207 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 338 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2830.41 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.44 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor all: 0.165 / Rfactor Rfree: 0.2026 / Rfactor Rwork: 0.1646 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.202 / Rfactor Rwork: 0.164 |