+Open data
-Basic information
Entry | Database: PDB / ID: 4of1 | ||||||
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Title | crystal structure of toxin from staphylococcus aureus Mu50 | ||||||
Components | mRNA interferase MazF | ||||||
Keywords | TOXIN / RNase | ||||||
Function / homology | Function and homology information endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Park, J.Y. / Im, H. / Seok, S.H. / Lee, B.J. | ||||||
Citation | Journal: To be Published Title: Structural Insights into the toxin from Staphylococcus aureus Mu50 Authors: Park, J.Y. / Im, H. / Seok, S.H. / 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 | 4of1.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4of1.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 4of1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/4of1 ftp://data.pdbj.org/pub/pdb/validation_reports/of/4of1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14535.858 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: mazF, SAV2068 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) References: UniProt: Q7A2N3, Hydrolases; Acting on ester bonds #2: Water | ChemComp-HOH / | |
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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: 3.37 Å3/Da / Density % sol: 63.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% w/v PEG 3350, 0.1 M Tris and 0.25 M lithium sulfate monohydrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2012 |
Radiation | Monochromator: DCM Si(111)crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→110.22 Å / Num. obs: 14620 / Redundancy: 15.5 % |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 0.189 / Num. unique all: 1441 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→110.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.134 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→110.22 Å
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Refine LS restraints |
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