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Yorodumi- PDB-4ax2: New Type VI-secreted toxins and self-resistance proteins in Serra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ax2 | ||||||
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Title | New Type VI-secreted toxins and self-resistance proteins in Serratia marcescens | ||||||
Components | RAP1B | ||||||
Keywords | TOXIN / RESISTANCE PROTEIN / HELICAL FOLD / S-SAD PHASING | ||||||
Function / homology | 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / IODIDE ION / Rap1b Function and homology information | ||||||
Biological species | SERRATIA MARCESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.88 Å | ||||||
Authors | English, G. / Trunk, K. / Rao, V.A. / Srikannathasan, V. / Fritsch, M.J. / Guo, M. / Hunter, W.N. / Coulthurst, S.J. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2012 Title: New Secreted Toxins and Immunity Proteins Encoded within the Type Vi Secretion System Gene Cluster of Serratia Marcescens Authors: English, G. / Trunk, K. / Rao, V.A. / Srikannathasan, V. / Hunter, W.N. / Coulthurst, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ax2.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ax2.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ax2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4ax2 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4ax2 | HTTPS FTP |
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-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: 16364.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Plasmid: PET15BTEV_PSC503 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-GAMI (DE3) / References: UniProt: K4DIE5*PLUS | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Nonpolymer details | IODIDE ION (IOD): HALIDE SOAK. IODIDES USED FOR SAD PHASING ALONG WITH S ATOMS. | Sequence details | GENOME IS NOT YET IN ANY DATABASE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.55M LI2SO4, 5% PEG 8000, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 24, 2011 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→67.5 Å / Num. obs: 14813 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.88→67.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.609 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / 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: 21.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→67.52 Å
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