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Yorodumi- PDB-3few: Structure and Function of Colicin S4, a colicin with a duplicated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3few | ||||||
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Title | Structure and Function of Colicin S4, a colicin with a duplicated receptor binding domain | ||||||
Components | Colicin S4 | ||||||
Keywords | IMMUNE SYSTEM / Colicin S4 / cell lysis / Y-ray / cell killing | ||||||
Function / homology | Function and homology information cytolysis / defense response to Gram-negative bacterium / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.45 Å | ||||||
Authors | Arnold, T. / Linke, D. / Zeth, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure and Function of Colicin S4, a Colicin with a Duplicated Receptor-binding Domain Authors: Arnold, T. / Zeth, K. / Linke, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3few.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3few.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 3few.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/3few ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3few | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 54977.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: Pet / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XB47 |
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#2: Chemical | ChemComp-NA / |
#3: 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: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.16M MgCl2, 24% PEG 4000, 20% glycerol, 80mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9761 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9761 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. all: 32353 / Num. obs: 32515 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.062 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5185 / Rsym value: 0.438 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.45→25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 13.96 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.255 / ESU R Free: 0.22 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.61 Å2 / Biso mean: 49.968 Å2 / Biso min: 14.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Total num. of bins used: 20
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