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Yorodumi- PDB-4wen: Co-complex structure of the F4 fimbrial adhesin FaeG variant ac w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wen | |||||||||
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Title | Co-complex structure of the F4 fimbrial adhesin FaeG variant ac with llama single domain antibody V2 | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Complex / Adhesin / Llama single domain antibody / Nanobody | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) Lama glama (llama) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Moonens, K. / Van den Broeck, I. / Pardon, E. / De Kerpel, M. / Remaut, H. / De Greve, H. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: Vet. Res. / Year: 2015 Title: Structural insight in the inhibition of adherence of F4 fimbriae producing enterotoxigenic Escherichia coli by llama single domain antibodies. Authors: Moonens, K. / Van den Broeck, I. / Okello, E. / Pardon, E. / De Kerpel, M. / Remaut, H. / De Greve, H. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013 Title: Orally fed seeds producing designer IgAs protect weaned piglets against enterotoxigenic Escherichia coli infection. Authors: Virdi, V. / Coddens, A. / De Buck, S. / Millet, S. / Goddeeris, B.M. / Cox, E. / De Greve, H. / Depicker, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wen.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wen.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/4wen ftp://data.pdbj.org/pub/pdb/validation_reports/we/4wen | HTTPS FTP |
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-Related structure data
Related structure data | 4wemC 4weuC 3hlrS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28993.223 Da / Num. of mol.: 1 / Fragment: UNP residues 20-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: faeG / Plasmid: pDEST14 / Details (production host): Gateway technology / Production host: Escherichia coli (E. coli) / References: UniProt: L7XD53, UniProt: P14190*PLUS |
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#2: Antibody | Mass: 13754.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / References: UniProt: R9VYW2 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100 mM Sodium Acetate pH 4.6, 200 mM ammonium sulfate, 25 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→47.74 Å / Num. obs: 36784 / % possible obs: 99.7 % / Redundancy: 20.2 % / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.89→2 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 1.4 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HLR Resolution: 1.89→47.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.867 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.539 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→47.74 Å
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Refine LS restraints |
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