+Open data
-Basic information
Entry | Database: PDB / ID: 8axy | |||||||||
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Title | Staphylococcus aureus endonuclease IV orthorhombic crystal form | |||||||||
Components | Probable endonuclease 4 | |||||||||
Keywords | HYDROLASE / endonuclease 4 / DNA repair / metalloenzyme | |||||||||
Function / homology | Function and homology information deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / DNA repair / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | |||||||||
Authors | Rouvinski, A. / Kirillov, S. / Saper, M.A. / Wiener, R. / Isupov, M.N. | |||||||||
Funding support | Israel, Kazakhstan, 2items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8axy.cif.gz | 263.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8axy.ent.gz | 207.4 KB | Display | PDB format |
PDBx/mmJSON format | 8axy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/8axy ftp://data.pdbj.org/pub/pdb/validation_reports/ax/8axy | HTTPS FTP |
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-Related structure data
Related structure data | 8eddC 1xp3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33215.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: nfo, SAR1634 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GGE2, deoxyribonuclease IV | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: - 0.1 M HEPES pH 7.0 - 2.2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→52.545 Å / Num. obs: 156665 / % possible obs: 99.1 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.882 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7372 / CC1/2: 0.319 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1xp3 Resolution: 1.05→52.545 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.164 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.024 / ESU R Free: 0.025 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.324 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→52.545 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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