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Yorodumi- PDB-4av5: Structure of a triclinic crystal of the FimH lectin domain in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4av5 | ||||||
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Title | Structure of a triclinic crystal of the FimH lectin domain in complex with a propynyl biphenyl alpha-D-mannoside, at 1.4 A resolution | ||||||
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 Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Wellens, A. / Lahmann, M. / Touaibia, M. / Vaucher, J. / Oscarson, S. / Roy, R. / Remaut, H. / Bouckaert, J. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: The Tyrosine Gate as a Potential Entropic Lever in the Receptor-Binding Site of the Bacterial Adhesin Fimh. Authors: Wellens, A. / Lahmann, M. / Touaibia, M. / Vaucher, J. / Oscarson, S. / Roy, R. / Remaut, H. / Bouckaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4av5.cif.gz | 265 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4av5.ent.gz | 218 KB | Display | PDB format |
PDBx/mmJSON format | 4av5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4av5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4av5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4av5_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 4av5_validation.cif.gz | 62 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4av5 ftp://data.pdbj.org/pub/pdb/validation_reports/av/4av5 | HTTPS FTP |
-Related structure data
Related structure data | 4auuC 4auyC 4av0C 4av4C 4avhC 4aviC 4avjC 4avkC 1uwfS 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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Unit cell |
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-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 4 / Fragment: LECTIN DOMAIN, RESIDUES 10-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68, UniProt: P08191*PLUS #2: Chemical | ChemComp-FYZ / ( #3: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.8 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 2% PEG8000, 0.5 M LI2SO4, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.918 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→18.79 Å / Num. obs: 109811 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.86 |
Reflection shell | Resolution: 1.4→1.6 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.83 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UWF Resolution: 1.4→18.592 Å / SU ML: 0.11 / σ(F): 2 / Phase error: 15.65 / 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: 12.123 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→18.592 Å
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Refine LS restraints |
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LS refinement shell |
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