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Yorodumi- PDB-4auj: FimH lectin domain co-crystal with a alpha-D-mannoside O-linked t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4auj | ||||||
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Title | FimH lectin domain co-crystal with a alpha-D-mannoside O-linked to para hydroxypropargyl phenyl | ||||||
Components | FIMH | ||||||
Keywords | SUGAR BINDING PROTEIN / 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: 1.527 Å | ||||||
Authors | Bouckaert, J. / Touaibia, M. / Roos, G. / Shiao, T.C. / Wang, Q. / Papadopoulos, A. / Roy, R. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2013 Title: Validation of Reactivity Descriptors to Assess the Aromatic Stacking within the Tyrosine Gate of Fimh. Authors: Roos, G. / Wellens, A. / Touaibia, M. / Yamakawa, N. / Geerlings, P. / Roy, R. / Wyns, L. / Bouchaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4auj.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4auj.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 4auj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4auj_validation.pdf.gz | 639 KB | Display | wwPDB validaton report |
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Full document | 4auj_full_validation.pdf.gz | 636.8 KB | Display | |
Data in XML | 4auj_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4auj_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4auj ftp://data.pdbj.org/pub/pdb/validation_reports/au/4auj | HTTPS FTP |
-Related structure data
Related structure data | 4attC 4buqC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16916.828 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 / Plasmid: PET24A / 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-HNW / |
#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: 1.97 Å3/Da / Density % sol: 37.68 % / Description: NONE |
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Crystal grow | Details: 70% 2 METHYL 2,4 PENTANE DIOL |
-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: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→48.17 Å / Num. obs: 21157 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 12.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.53→1.6 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.3 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UWF Resolution: 1.527→31.78 Å / SU ML: 0.16 / σ(F): 1.4 / Phase error: 15.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.473 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.527→31.78 Å
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Refine LS restraints |
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LS refinement shell |
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