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Yorodumi- PDB-1n12: Crystal structure of the PapE (N-terminal-deleted) pilus subunit ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n12 | ||||||
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Title | Crystal structure of the PapE (N-terminal-deleted) pilus subunit bound to a peptide corresponding to the N-terminal extension of the PapK pilus subunit (residues 1-11) from uropathogenic E. coli | ||||||
Components |
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Keywords | CHAPERONE / Immunoglobulin-like fold / donor strand complementation / donor strand exchange / chaperone priming / pilus fiber assembly / organelle biogenesis | ||||||
Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å | ||||||
Authors | Sauer, F.G. / Pinkner, J.S. / Waksman, G. / Hultgren, S.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n12.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n12.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n12_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
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Full document | 1n12_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 1n12_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1n12_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n12 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n12 | HTTPS FTP |
-Related structure data
-Links
-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: 14832.035 Da / Num. of mol.: 2 / Fragment: residue 25-173, residue 26-36 deleted Mutation: N-terminal residue 26-36 deleted, contains selenomethionine at methionine positions Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P08407 #2: Protein/peptide | Mass: 1207.315 Da / Num. of mol.: 2 / Fragment: residue 22-32 / Source method: obtained synthetically / Details: synthesized peptide / References: UniProt: P42190, UniProt: P42191*PLUS #3: 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: 1.75 Å3/Da / Density % sol: 29.19 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8.5 Details: 100 mM Tris pH 8.5, 200 mM NaCl, 27-32% PEG 4000, 1 mM beta-mercaptoethanol, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9667 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9667 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 8 Å2 |
Reflection | *PLUS Highest resolution: 1.87 Å / Lowest resolution: 30 Å / Num. obs: 18969 / % possible obs: 99.2 % / Num. measured all: 232749 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 96.8 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 8.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.87→26.21 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.9399 Å2 / ksol: 0.348785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→26.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.99 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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