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Yorodumi- PDB-4w6x: Co-complex structure of the lectin domain of F18 fimbrial adhesin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w6x | |||||||||
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Title | Co-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF7 | |||||||||
Components |
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Keywords | CELL ADHESION / Lectin / Fimbriae / Inhibitor | |||||||||
Function / homology | Jelly Rolls - #1210 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / F18 fimbrial adhesin AC Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) Lama glama (llama) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||
Authors | Moonens, K. / De Kerpel, M. / Coddens, A. / Cox, E. / Pardon, E. / Remaut, H. / De Greve, H. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: Plos One / Year: 2014 Title: Nanobody Mediated Inhibition of Attachment of F18 Fimbriae Expressing Escherichia coli. Authors: Moonens, K. / De Kerpel, M. / Coddens, A. / Cox, E. / Pardon, E. / Remaut, H. / De Greve, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w6x.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w6x.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 4w6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w6x_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 4w6x_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 4w6x_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4w6x_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/4w6x ftp://data.pdbj.org/pub/pdb/validation_reports/w6/4w6x | HTTPS FTP |
-Related structure data
Related structure data | 4w6wC 4w6yC 2x1oS 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: 16311.161 Da / Num. of mol.: 1 / Fragment: UNP Residues 35-185 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fedF / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: Q47212 |
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#2: Antibody | Mass: 14311.772 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pDESTR4-R3 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1 M (NH4)2 SO4, 90 mM Na-citrate pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 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: 1.88→44.77 Å / Num. obs: 21548 / % possible obs: 97.4 % / Redundancy: 5.7 % / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2703 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X1O Resolution: 1.88→63.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.085 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 31.457 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→63.75 Å
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Refine LS restraints |
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