+Open data
-Basic information
Entry | Database: PDB / ID: 3tuf | ||||||
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Title | Structure of the SpoIIQ-SpoIIIAH pore forming complex. | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Intercellular signalling / intercellular channel / sporulation / Cell engulfment and signalling / Intercellular Space | ||||||
Function / homology | Function and homology information endospore-forming forespore / sporulation resulting in formation of a cellular spore / metalloendopeptidase activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 Å | ||||||
Authors | Levdikov, V.M. / Blagova, E.V. / Wilkinson, A.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structure of components of an intercellular channel complex in sporulating Bacillus subtilis. Authors: Levdikov, V.M. / Blagova, E.V. / McFeat, A. / Fogg, M.J. / Wilson, K.S. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tuf.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tuf.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tuf_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 3tuf_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 3tuf_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 3tuf_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/3tuf ftp://data.pdbj.org/pub/pdb/validation_reports/tu/3tuf | HTTPS FTP |
-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
#1: Protein | Mass: 26414.461 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU36550, spoIIQ, ywnI / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P71044 |
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#2: Protein | Mass: 21238.254 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU24360, spoIIIAH / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P49785 |
#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: 3.12 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate,50% PEG 400, 0.5 mM spermidine, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Monochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. all: 23724 / Num. obs: 23724 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 32.1 |
-Processing
Software |
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Refinement | Resolution: 2.26→46.72 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 |
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Refinement step | Cycle: LAST / Resolution: 2.26→46.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.323 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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