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- PDB-4avi: Structure of the FimH lectin domain in the trigonal space group, ... -
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Open data
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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 | ||||||
![]() | FIMH | ||||||
![]() | CELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wellens, A. / Lahmann, M. / Touaibia, M. / Vaucher, J. / Oscarson, S. / Roy, R. / Remaut, H. / Bouckaert, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.8 KB | Display | ![]() |
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PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 877.6 KB | Display | ![]() |
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Full document | ![]() | 881.1 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4auuC ![]() 4auyC ![]() 4av0C ![]() 4av4C ![]() 4av5C ![]() 4avhC ![]() 4avjC ![]() 4avkC ![]() 2vcoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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