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- PDB-2nq9: High resolution crystal structure of Escherichia coli endonucleas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nq9 | ||||||
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Title | High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA | ||||||
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![]() | HYDROLASE/DNA / TIM-barrel / trinuclear Zn active site / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding ...deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcin-Hosfield, E.D. / Hosfield, D.J. / Tainer, J.A. | ||||||
![]() | ![]() Title: DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Authors: Garcin, E.D. / Hosfield, D.J. / Desai, S.A. / Haas, B.J. / Bjoras, M. / Cunningham, R.P. / Tainer, J.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.1 KB | Display | ![]() |
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PDB format | ![]() | 62.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 449.7 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nqhC ![]() 2nqjC ![]() 1qtwS S: Starting model for refinement C: citing same article ( |
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Similar 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
-DNA chain , 3 types, 3 molecules BCD
#1: DNA chain | Mass: 1783.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1394.951 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3372.234 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 31426.402 Da / Num. of mol.: 1 / Mutation: Y72A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 2 types, 349 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% MPEG-2000, 0.1 M HEPES pH 7, and 0.4 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→20 Å / Num. obs: 78368 / % possible obs: 98 % / Observed criterion σ(I): 278343 / Rsym value: 0.098 / Net I/σ(I): 18.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1QTW Resolution: 1.45→20 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.01
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