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Yorodumi- PDB-4j3o: Crystal structure of the FimD usher traversed by the pilus tip co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j3o | ||||||
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Title | Crystal structure of the FimD usher traversed by the pilus tip complex assembly composed of FimC:FimF:FimG:FimH | ||||||
Components |
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Keywords | CELL ADHESION/CHAPERONE/MEMBRANE PROTEIN / beta barrel / immunglobuline-like fold / type 1 pilus assembly / pilus subunit translocation / adhesion / D-Mannose-binding / bacterial outer membrane / CELL ADHESION-CHAPERONE-MEMBRANE PROTEIN complex | ||||||
Function / homology | Function and homology information fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / mannose binding / host cell membrane / chaperone-mediated protein folding ...fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / mannose binding / host cell membrane / chaperone-mediated protein folding / protein folding chaperone / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space / cell adhesion Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Geibel, S. / Waksman, G. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structural and energetic basis of folded-protein transport by the FimD usher. Authors: Geibel, S. / Procko, E. / Hultgren, S.J. / Baker, D. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j3o.cif.gz | 306.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j3o.ent.gz | 246 KB | Display | PDB format |
PDBx/mmJSON format | 4j3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j3o ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j3o | HTTPS FTP |
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-Related 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: 14864.227 Da / Num. of mol.: 1 / Fragment: UNP residues 24-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimG, b4319, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190 |
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#2: Protein | Mass: 29081.314 Da / Num. of mol.: 1 / Fragment: UNP residues 22-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191 |
#3: Protein | Mass: 23582.914 Da / Num. of mol.: 1 / Fragment: UNP residues 37-241 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimC, b4316, JW4279 / Production host: Escherichia coli (E. coli) / References: UniProt: P31697 |
#4: Protein | Mass: 16177.095 Da / Num. of mol.: 1 / Fragment: UNP residues 21-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimF, b4318, JW4281 / Production host: Escherichia coli (E. coli) / References: UniProt: P08189 |
#5: Protein | Mass: 92640.227 Da / Num. of mol.: 1 / Fragment: UNP residues 46-878 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimD, b4317, JW5780 / Production host: Escherichia coli (E. coli) / References: UniProt: P30130 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010 / Details: mirrors |
Radiation | Monochromator: Si111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→83.67 Å / Num. all: 25518 / Num. obs: 25474 / % possible obs: 99.84 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.8→3.9 Å / % possible all: 99.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BWU for FimC:FimF, PDB 3RFZ for FimD, PDB 3JWN for FimG:FimH Resolution: 3.8→83.668 Å / SU ML: 0.76 / σ(F): 1.33 / Phase error: 37.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→83.668 Å
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Refine LS restraints |
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LS refinement shell |
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