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- PDB-1n0l: Crystal structure of the PapD chaperone (C-terminally 6x histidin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n0l | ||||||
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Title | Crystal structure of the PapD chaperone (C-terminally 6x histidine-tagged) bound to the PapE pilus subunit (N-terminal-deleted) from uropathogenic E. coli | ||||||
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![]() | CHAPERONE / Immunoglobulin-like fold / donor strand complemenation / donor strand exchange / chaperone priming / pilus fiber assembly | ||||||
Function / homology | ![]() cell adhesion involved in single-species biofilm formation / pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sauer, F.G. / Pinkner, J.S. / Waksman, G. / Hultgren, S.J. | ||||||
![]() | ![]() Title: Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation Authors: Sauer, F.G. / Pinkner, J.S. / Waksman, G. / Hultgren, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.2 KB | Display | ![]() |
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PDB format | ![]() | 113.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.9 KB | Display | ![]() |
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Full document | ![]() | 482.5 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 25559.463 Da / Num. of mol.: 2 / Fragment: residues 22-239 Mutation: 6x histidine tag at C-terminus, selenomethionine at methionine positions Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14832.035 Da / Num. of mol.: 2 / Fragment: residues 25-173, residues 26-36 deleted Mutation: N-terminal residues 26-36 deleted , selenomethionine at methionine positions Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.08 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 250 mM MgCl2, 17-18% PEG 4000, 4-7% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 27884 / % possible obs: 91 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.041 / Net I/σ(I): 28.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 162110 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 91.5 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 6.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.3694 Å2 / ksol: 0.309847 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→24.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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