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Open data
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Basic information
Entry | Database: PDB / ID: 8edd | |||||||||
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Title | Staphylococcus aureus endonuclease IV Y33F mutant | |||||||||
![]() | Probable endonuclease 4 | |||||||||
![]() | HYDROLASE / endonuclease 4 / DNA repair / metalloenzyme / mutant | |||||||||
Function / homology | ![]() deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saper, M.A. / Kirillov, S. / Isupov, M.N. / Wiener, R. / Rouvinski, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Octahedrally coordinated iron in the catalytic site of endonuclease IV from Staphylococcus aureus Authors: Kirillov, S. / Isupov, M.N. / Paterson, N. / Wiener, R. / Abeldenov, S. / Saper, M.A. / Rouvinski, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215 KB | Display | ![]() |
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PDB format | ![]() | 147.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8axySC ![]() 8pkbC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33199.539 Da / Num. of mol.: 1 / Mutation: Y33F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 203 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % / Description: needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein in 20 mM phosphate. Precipitant: 20-30% polyethylene glycol 3350, 200 mM NaCl, 100 mM BisTris, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 150 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→152.77 Å / Num. obs: 41699 / % possible obs: 100 % / Redundancy: 13.19 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.189 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 13.51 % / Rmerge(I) obs: 3.394 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2173 / CC1/2: 0.305 / Rpim(I) all: 0.955 / Rrim(I) all: 3.527 / % possible all: 99.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8AXY Resolution: 1.5→40.49 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2523 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40.49 Å
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Refine LS restraints |
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LS refinement shell |
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