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Yorodumi- PDB-1ze3: Crystal Structure of the Ternary Complex of FIMD (N-Terminal Doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ze3 | ||||||
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Title | Crystal Structure of the Ternary Complex of FIMD (N-Terminal Domain) with FIMC and the Pilin Domain of FIMH | ||||||
Components |
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Keywords | CHAPERONE/STRUCTURAL/MEMBRANE PROTEIN / Usher / soluble domain / ternary complex with chaperone and pilus subunit / CHAPERONE-STRUCTURAL-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 / D-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 / D-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: 1.84 Å | ||||||
Authors | Nishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Grutter, M.G. / Wuthrich, K. ...Nishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Grutter, M.G. / Wuthrich, K. / Glockshuber, R. / Capitani, G. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. Authors: Nishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Glockshuber, R. / Capitani, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ze3.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ze3.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 1ze3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/1ze3 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/1ze3 | HTTPS FTP |
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-Related structure data
Related structure data | 1zdvC 1zdxC 1qunS S: Starting model for refinement C: citing same article (ref.) |
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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: 22754.031 Da / Num. of mol.: 1 / Fragment: FimC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC / Plasmid: pCT-FimH-FimC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P31697 | ||
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#2: Protein | Mass: 12283.583 Da / Num. of mol.: 1 / Fragment: FimH pilin domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: pCT-FimH-FimC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191 | ||
#3: Protein | Mass: 13664.263 Da / Num. of mol.: 1 / Fragment: FimD N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD / Plasmid: pFimDn (1-125) / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P30130 | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 6000, MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.843→33.615 Å / Num. obs: 44185 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.84→1.91 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.363 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MODEL DERIVED FROM PDB ENTRY 1QUN Resolution: 1.84→33.7 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.84→33.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.91 Å
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