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Yorodumi- PDB-5fx3: Breaking down the wall: mutation of the tyrosine gate of the univ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fx3 | |||||||||
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Title | Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH | |||||||||
Components | FimH | |||||||||
Keywords | CELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD | |||||||||
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 / cell adhesion / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Bouckaert, J. | |||||||||
Citation | Journal: IUCrJ / Year: 2017 Title: Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding. Authors: Rabbani, S. / Krammer, E.M. / Roos, G. / Zalewski, A. / Preston, R. / Eid, S. / Zihlmann, P. / Prevost, M. / Lensink, M.F. / Thompson, A. / Ernst, B. / Bouckaert, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fx3.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fx3.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fx3_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5fx3_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5fx3_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 5fx3_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fx3 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fx3 | HTTPS FTP |
-Related structure data
Related structure data | 4ca4C 5fs5C 5fwrC 4auuS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16865.762 Da / Num. of mol.: 1 / Fragment: FIMH LECTIN DOMAIN, RESIDUES 22-179 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9S497, UniProt: P08191*PLUS | ||
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#2: Chemical | ChemComp-EDT / {[-( | ||
#3: Water | ChemComp-HOH / | ||
Has protein modification | Y | ||
Nonpolymer details | {[-(BIS-CARBOXYMETSequence details | Y137A MUTATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.76 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M SODIUM MALONATE 0.1 M BIS TRIS PROPANE PH 7.5 20 % W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→46.92 Å / Num. obs: 21963 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 17.64 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.27 |
Reflection shell | Resolution: 1.91→2.04 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AUU Resolution: 1.9→46.921 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 18.98 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.921 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.6199 Å / Origin y: -15.2282 Å / Origin z: 3.7566 Å
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Refinement TLS group | Selection details: ALL |