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Yorodumi- PDB-5aap: Complex of the FimH lectin with a C-linked para-biphenyl methylen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aap | |||||||||
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Title | Complex of the FimH lectin with a C-linked para-biphenyl methylene alpha-D-mannoside | |||||||||
Components | FIMH | |||||||||
Keywords | CELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD | |||||||||
Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / cell adhesion Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 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 | 5aap.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aap.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 5aap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aap_validation.pdf.gz | 661.6 KB | Display | wwPDB validaton report |
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Full document | 5aap_full_validation.pdf.gz | 662 KB | Display | |
Data in XML | 5aap_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 5aap_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/5aap ftp://data.pdbj.org/pub/pdb/validation_reports/aa/5aap | HTTPS FTP |
-Related structure data
Related structure data | 5aalC 5abzC 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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Unit cell |
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-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 1 / Fragment: LECTIN DOMAIN, UNP 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: Q1R2J4*PLUS |
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#2: Chemical | ChemComp-VNY / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 1.87 Å3/Da / Density % sol: 34.2 % / 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→41 Å / Num. obs: 26776 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 6.58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.91 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.85 / % possible all: 39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AUU Resolution: 1.302→38.331 Å / SU ML: 0.08 / σ(F): 2.01 / Phase error: 13.86 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.302→38.331 Å
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Refine LS restraints |
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LS refinement shell |
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