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Yorodumi- PDB-4av4: FimH lectin domain co-crystal with a alpha-D-mannoside O-linked t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4av4 | ||||||
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Title | FimH lectin domain co-crystal with a alpha-D-mannoside O-linked to a propynyl pyridine | ||||||
Components | FIMH | ||||||
Keywords | CELL ADHESION / FIMBRIAE / VARIABLE IMMUNOGLOBULIN FOLD / URINARY TRACT INFECTION | ||||||
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: 1.9 Å | ||||||
Authors | Bouckaert, J. / Touaibia, M. / Roos, G. / Shiao, T.C. / Wang, Q. / Papadopoulos, A. / Roy, R. | ||||||
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 | 4av4.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4av4.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 4av4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4av4_validation.pdf.gz | 679.9 KB | Display | wwPDB validaton report |
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Full document | 4av4_full_validation.pdf.gz | 679.9 KB | Display | |
Data in XML | 4av4_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 4av4_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4av4 ftp://data.pdbj.org/pub/pdb/validation_reports/av/4av4 | HTTPS FTP |
-Related structure data
Related structure data | 4auuC 4auyC 4av0C 4av5C 4avhC 4aviC 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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Unit cell |
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-Components
#1: Protein | Mass: 16915.842 Da / Num. of mol.: 1 / 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 |
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#2: Sugar | ChemComp-FVQ / |
#3: 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: 1.86 Å3/Da / Density % sol: 33.86 % / Description: NONE |
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Crystal grow | pH: 8.6 Details: 30 % (V/V) 2-PROPANOL, 100 MM TRIS-HCL PH 8.5, 200 MM AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0 |
Reflection | Resolution: 1.9→38.3 Å / Num. obs: 11106 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.23 |
Reflection shell | Resolution: 1.9→2.09 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.18 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VCO Resolution: 1.9→38.332 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 24.28 / 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: 35.688 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→38.332 Å
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Refine LS restraints |
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LS refinement shell |
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