+Open data
-Basic information
Entry | Database: PDB / ID: 7ewi | ||||||
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Title | Toxin protein from Staphylococcus aureus | ||||||
Components | Endoribonuclease MazF | ||||||
Keywords | TOXIN / hydrolase RNase | ||||||
Function / homology | mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / DNA binding / PHOSPHATE ION / Endoribonuclease MazF Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Kim, D.H. / Kang, S.M. / Lee, S.J. / Lee, B.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Role of PemI in the Staphylococcus aureus PemIK toxin-antitoxin complex: PemI controls PemK by acting as a PemK loop mimic. Authors: Kim, D.H. / Kang, S.M. / Baek, S.M. / Yoon, H.J. / Jang, D.M. / Kim, H.S. / Lee, S.J. / Lee, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ewi.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ewi.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ewi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/7ewi ftp://data.pdbj.org/pub/pdb/validation_reports/ew/7ewi | HTTPS FTP |
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-Related structure data
Related structure data | 7ewjC 1m1fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13459.659 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SACH_a18 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PFJ6 #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) PEG 1000, 0.1 M potassium phosphate monobasic/sodium phosphate dibasic, pH 6.2, 0.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40 Å / Num. obs: 37045 / % possible obs: 97.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.988 / Net I/σ(I): 24.13 |
Reflection shell | Resolution: 1.94→1.97 Å / Num. unique obs: 1462 / CC1/2: 0.877 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M1F Resolution: 1.93→33.95 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→33.95 Å
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Refine LS restraints |
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LS refinement shell |
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