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Yorodumi- PDB-4avi: Structure of the FimH lectin domain in the trigonal space group, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4avi | ||||||
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Title | Structure of the FimH lectin domain in the trigonal space group, in complex with a methyl ester octyl alpha-D-mannoside at 2.4 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: 2.4 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 | 4avi.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4avi.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 4avi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4avi_validation.pdf.gz | 877.6 KB | Display | wwPDB validaton report |
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Full document | 4avi_full_validation.pdf.gz | 881.1 KB | Display | |
Data in XML | 4avi_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4avi_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4avi ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avi | HTTPS FTP |
-Related structure data
Related structure data | 4auuC 4auyC 4av0C 4av4C 4av5C 4avhC 4avjC 4avkC 2vcoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 2 / 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 | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: 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: 2.78 Å3/Da / Density % sol: 55.76 % / Description: NONE |
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Crystal grow | pH: 8.6 Details: 1 M LI2SO4, 100 MM TRIS PH 8.6, 10 MM NICL2, 0.2 M NON-DETERGENT SULFOBETAINE 201 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.873 |
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: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→18.64 Å / Num. obs: 15111 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 24.75 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.01 |
Reflection shell | Resolution: 2.4→2.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VCO Resolution: 2.4→18.64 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 19.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.604 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→18.64 Å
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Refine LS restraints |
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LS refinement shell |
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