+Open data
-Basic information
Entry | Database: PDB / ID: 6af3 | ||||||
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Title | Toxin-Antitoxin module from Streptococcus pneumoniae | ||||||
Components |
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Keywords | TOXIN / Toxin-Antitoxin complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.803 Å | ||||||
Authors | Kang, S.M. / Kim, D.H. / Jin, C. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Toxin-Antitoxin module from Streptococcus pneumoniae Authors: Kang, S.M. / Kim, D.H. / Jin, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6af3.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6af3.ent.gz | 148.8 KB | Display | PDB format |
PDBx/mmJSON format | 6af3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/6af3 ftp://data.pdbj.org/pub/pdb/validation_reports/af/6af3 | HTTPS FTP |
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-Related 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: 16981.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Strain: TIGR4 / Gene: higB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UQ08 #2: Protein | Mass: 10999.912 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Strain: TIGR4 / Gene: higA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UQ20 #3: 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: 1.96 Å3/Da / Density % sol: 37.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20%(w/v) PEG 1000, 0.1M potassium phosphate monobasic/sodium phosphate dibasic, pH 6.2, 0.2M sodium chloride |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 41486 / % possible obs: 99.9 % / Redundancy: 11 % / Rpim(I) all: 0.043 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 2066 / Rpim(I) all: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.803→49.795 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.803→49.795 Å
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Refine LS restraints |
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LS refinement shell |
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