+Open data
-Basic information
Entry | Database: PDB / ID: 5cul | ||||||
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Title | crystal structure of the PscU C-terminal domain | ||||||
Components | Translocation protein in type III secretion | ||||||
Keywords | CELL INVASION / secretion system | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Bergeron, J.R.C. / Strynadka, N.C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: The Structure of a Type 3 Secretion System (T3SS) Ruler Protein Suggests a Molecular Mechanism for Needle Length Sensing. Authors: Bergeron, J.R. / Fernandez, L. / Wasney, G.A. / Vuckovic, M. / Reffuveille, F. / Hancock, R.E. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cul.cif.gz | 36.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cul.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cul_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
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Full document | 5cul_full_validation.pdf.gz | 425.2 KB | Display | |
Data in XML | 5cul_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 5cul_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/5cul ftp://data.pdbj.org/pub/pdb/validation_reports/cu/5cul | HTTPS FTP |
-Related structure data
Related structure data | 5cukC 2jliS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 14434.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pscU, PA1690 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I337 #2: 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: 1.44 Å3/Da / Density % sol: 14.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1M di-ammonium hydrogen phosphate, 0.1 M sodium acetate, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→42.66 Å / Num. obs: 3694 / % possible obs: 99.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.387 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.799 / Num. unique all: 536 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JLI Resolution: 2.9→42.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.79 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 2.042 / ESU R Free: 0.327 / 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: 53.794 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→42.66 Å
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Refine LS restraints |
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