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Yorodumi- PDB-4igl: Structure of the RHS-repeat containing BC component of the secret... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4igl | ||||||
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Title | Structure of the RHS-repeat containing BC component of the secreted ABC toxin complex from Yersinia entomophaga | ||||||
Components |
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Keywords | TOXIN / Beta-Propeller / RHS / toxin complex / Toxin transporter/chaperone / Secreted | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å | ||||||
Authors | Busby, J.N. / Panjikar, S. / Landsberg, M.J. / Hurst, M.R.H. / Lott, J.S. | ||||||
Citation | Journal: Nature / Year: 2013 Title: The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device Authors: Busby, J.N. / Panjikar, S. / Landsberg, M.J. / Hurst, M.R.H. / Lott, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4igl.cif.gz | 889.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4igl.ent.gz | 704.7 KB | Display | PDB format |
PDBx/mmJSON format | 4igl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4igl_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 4igl_full_validation.pdf.gz | 515 KB | Display | |
Data in XML | 4igl_validation.xml.gz | 163.1 KB | Display | |
Data in CIF | 4igl_validation.cif.gz | 235.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/4igl ftp://data.pdbj.org/pub/pdb/validation_reports/ig/4igl | HTTPS FTP |
-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: 167205.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cloned into MCS1 / Source: (gene. exp.) Yersinia (bacteria) / Strain: MH-1 / Gene: yenB / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A880 #2: Protein | Mass: 76385.539 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-690 Source method: isolated from a genetically manipulated source Details: Cloned into MCS2 / Source: (gene. exp.) Yersinia (bacteria) / Strain: MH-1 / Gene: yenC2 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A882 #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-K / #5: 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: 2.78 Å3/Da / Density % sol: 55.73 % / Mosaicity: 0.22 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 18% PEG 3350, 150mM potassium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953694 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 2, 2012 | ||||||||||||||||||||||||
Radiation | Monochromator: Double Si(111) with sagittaly bent second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953694 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.264→137.177 Å / Num. all: 245045 / Num. obs: 245045 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 37.31 Å2 / Rmerge(I) obs: 0.3 / Rsym value: 0.3 / Net I/σ(I): 9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Autobuilt model of non-isomorphous crystal solved by SeMet MAD Resolution: 2.49→49.549 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8228 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.12 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.94 Å2 / Biso mean: 48.6889 Å2 / Biso min: 28.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→49.549 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %
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