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Yorodumi- PDB-4j30: Structure of the effector - immunity system Tae4 / Tai4 from Salm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j30 | ||||||
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Title | Structure of the effector - immunity system Tae4 / Tai4 from Salmonella typhimurium, selenomethionine variant | ||||||
Components |
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Keywords | TOXIN/INHIBITOR / N1pC/P60 papain like cysteine peptidase Tae4 / peptidoglycan hydrolase / immunity protein Tai4 / Tae4: cytoplasmatic / Tai4: periplasmatic / TOXIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex ...endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Benz, J. / Reinstein, J. / Meinhart, A. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structural Insights into the Effector - Immunity System Tae4/Tai4 from Salmonella typhimurium. Authors: Benz, J. / Reinstein, J. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j30.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j30.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 4j30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j30_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 4j30_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 4j30_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4j30_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j30 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j30 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19603.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q93IS4 | ||
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#2: Protein | Mass: 11758.077 Da / Num. of mol.: 1 Fragment: periplasmatic inhibitor domain (UNP residues 27-127) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q8ZRL5 | ||
#3: Chemical | ChemComp-FLC / | ||
#4: Chemical | ChemComp-ETX / #5: Water | ChemComp-HOH / | |
-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: 63.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 200 mM tri-sodium citrate pH 6.0, 30 % (v/v) 2-ethoxyethanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97933 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2012 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 36560 / Num. obs: 36560 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 43 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 7.1 / Num. unique all: 4358 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→37.8 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.127 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.882 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→37.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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