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Yorodumi- PDB-5o68: Crystal Structure of the Pseudomonas functional amyloid secretion... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o68 | |||||||||
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Title | Crystal Structure of the Pseudomonas functional amyloid secretion protein FapF - R157A mutant | |||||||||
Components | FapF | |||||||||
Keywords | MEMBRANE PROTEIN / amyloid / secretion / plug / barrel | |||||||||
Function / homology | Autotransporter beta-domain superfamily / FapF Function and homology information | |||||||||
Biological species | Pseudomonas sp. UK4 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | |||||||||
Authors | Rouse, S.L. / Hare, S. / Lambert, S. / Morgan, R.M.L. / Hawthorne, W.J. / Berry, J. / Matthews, S.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2017 Title: A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Authors: Rouse, S.L. / Hawthorne, W.J. / Berry, J.L. / Chorev, D.S. / Ionescu, S.A. / Lambert, S. / Stylianou, F. / Ewert, W. / Mackie, U. / Morgan, R.M.L. / Otzen, D. / Herbst, F.A. / Nielsen, P.H. ...Authors: Rouse, S.L. / Hawthorne, W.J. / Berry, J.L. / Chorev, D.S. / Ionescu, S.A. / Lambert, S. / Stylianou, F. / Ewert, W. / Mackie, U. / Morgan, R.M.L. / Otzen, D. / Herbst, F.A. / Nielsen, P.H. / Dueholm, M. / Bayley, H. / Robinson, C.V. / Hare, S. / Matthews, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o68.cif.gz | 592.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o68.ent.gz | 481.2 KB | Display | PDB format |
PDBx/mmJSON format | 5o68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o68_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5o68_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5o68_validation.xml.gz | 102.8 KB | Display | |
Data in CIF | 5o68_validation.cif.gz | 140.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/5o68 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/5o68 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 36365.086 Da / Num. of mol.: 12 / Mutation: R157A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. UK4 (bacteria) / Gene: fapF, PSUK4_00060 / Plasmid: PRSF1b / Details (production host): OmpA leader sequence / Production host: Escherichia coli (E. coli) / References: UniProt: C4IN73 #2: Chemical | ChemComp-C8E / ( #3: Chemical | ChemComp-LDA / |
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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: 4.02 Å3/Da / Density % sol: 69.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0/05 - 0.1 M sodium citrate, 0.1 M sodium chloride, 20-30 % PEG400 PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→91.7 Å / Num. obs: 94515 / % possible obs: 99.02 % / Redundancy: 3.35 % / Rpim(I) all: 0.103 / Net I/σ(I): 3.49 |
Reflection shell | Resolution: 3.08→3.13 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Rpim(I) all: 0.5 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 5065 / Resolution: 3.08→91.73 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / SU B: 34.4 / SU ML: 0.582 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / 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: 44.567 Å2
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Refinement step | Cycle: 1 / Resolution: 3.08→91.73 Å
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