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Yorodumi- PDB-1kiu: FimH adhesin Q133N mutant-FimC chaperone complex with methyl-alph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kiu | ||||||
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Title | FimH adhesin Q133N mutant-FimC chaperone complex with methyl-alpha-D-mannose | ||||||
Components |
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Keywords | CHAPERONE/CELL ADHESION / adhesin-chaperone complex / mannose-bound / CHAPERONE-CELL ADHESION COMPLEX | ||||||
Function / homology | Function and homology information pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / chaperone-mediated protein folding / protein folding chaperone / cell wall organization ...pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / chaperone-mediated protein folding / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Hung, C.S. / Bouckaert, J. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2002 Title: Structural basis of tropism of Escherichia coli to the bladder during urinary tract infection. Authors: Hung, C.S. / Bouckaert, J. / Hung, D. / Pinkner, J. / Widberg, C. / DeFusco, A. / Auguste, C.G. / Strouse, R. / Langermann, 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 | 1kiu.cif.gz | 711.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kiu.ent.gz | 604 KB | Display | PDB format |
PDBx/mmJSON format | 1kiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kiu_validation.pdf.gz | 597.7 KB | Display | wwPDB validaton report |
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Full document | 1kiu_full_validation.pdf.gz | 918.2 KB | Display | |
Data in XML | 1kiu_validation.xml.gz | 174 KB | Display | |
Data in CIF | 1kiu_validation.cif.gz | 234.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/1kiu ftp://data.pdbj.org/pub/pdb/validation_reports/ki/1kiu | HTTPS FTP |
-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 22724.049 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC / Plasmid: pMMB60 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P31697 #2: Protein | Mass: 29067.287 Da / Num. of mol.: 8 / Mutation: Q133N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: pMMB60 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P08191 #3: Sugar | ChemComp-MMA / #4: 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: 2.46 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: ammonium sulphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 297K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 20, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.46 Å / Num. all: 71767 / Num. obs: 72289 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3→3.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.51 / % possible all: 87 |
Reflection | *PLUS Lowest resolution: 45 Å / % possible obs: 87.1 % / Num. measured all: 197848 |
Reflection shell | *PLUS Lowest resolution: 3.11 Å / % possible obs: 65.9 % / Rmerge(I) obs: 0.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 56.0908 Å2 / ksol: 0.317169 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→45 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: restrained / Weight Biso : 10 / Weight position: 300 | |||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 45 Å / Rfactor Rfree: 0.28 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.39 / Rfactor Rwork: 0.36 / Rfactor obs: 0.36 |