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Yorodumi- PDB-5abz: Complex of the FimH lectin with a C-linked naphtyl alpha-D-mannos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5abz | |||||||||
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Title | Complex of the FimH lectin with a C-linked naphtyl alpha-D-mannoside in soaked trigonal crystals at 2.40 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 | de Ruyck, J. / Bouckaert, J. | |||||||||
Citation | Journal: Iucrj / Year: 2016 Title: Structures of C-Mannosylated Anti-Adhesives Bound to the Type 1 Fimbrial Fimh Adhesin Authors: De Ruyck, J. / Lensink, M.F. / Bouckaert, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5abz.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5abz.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 5abz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5abz ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5abz | HTTPS FTP |
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-Related structure data
Related structure data | 5aalC 5aapC 4auuS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 2 / Fragment: LECTIN DOMAIN, UNP RESIDUES 22-179 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: P08191 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | (2R,3S,4R,5S, 6R)-2-(HYDROXYMETHYL)-6-[3-(NAPHTHALEN-1-YL)PROPYL]OXANE-3, 4,5-TRIOL (247): ANTI- ...(2R,3S,4R,5S, 6R)-2-(HYDROXYMET | |
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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: 2.81 Å3/Da / Density % sol: 56.24 % / Description: NONE |
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Crystal grow | pH: 8.6 / Details: PH 8.6 |
-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: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.48 Å / Num. obs: 15226 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 24.72 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.4→2.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AUU Resolution: 2.4→39.479 Å / SU ML: 0.24 / σ(F): 2.01 / Phase error: 19.18 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.479 Å
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Refine LS restraints |
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LS refinement shell |
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