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Yorodumi- PDB-8eln: Crystal Structure of Nanobody VHH222 Bound to Its Antigen PA14 Cif -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eln | ||||||||||||||||||
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Title | Crystal Structure of Nanobody VHH222 Bound to Its Antigen PA14 Cif | ||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Pseudomonas aeruginosa / nanobody VHH / immunoglobulin domain / CFTR inhibitory factor (Cif) | ||||||||||||||||||
Function / homology | Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / CFTR inhibitory factor Function and homology information | ||||||||||||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) Vicugna pacos (alpaca) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||||||||
Authors | Simard, A.R. / Madden, D.R. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: To Be Published Title: Crystal Structure of Nanobody VHH222 Bound to Its Antigen PA14 Cif Authors: Simard, A.R. / Madden, D.R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eln.cif.gz | 496 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eln.ent.gz | 403.7 KB | Display | PDB format |
PDBx/mmJSON format | 8eln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/8eln ftp://data.pdbj.org/pub/pdb/validation_reports/el/8eln | HTTPS FTP |
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-Related structure data
Related structure data | 3kd2S 8e1cS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34164.699 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA2394 / Plasmid: pDPM73 / Details (production host): C-terminal 6X-His / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26 #2: Antibody | Mass: 13531.143 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET16b / Details (production host): N-terminal 10X-His SUMO fusion / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL #3: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.25 % |
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Crystal grow | Temperature: 292.8 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20% (w/v) PEG4000, 200 mM ammonium acetate, 100 mM sodium acetate, pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.44 Å / Num. obs: 101735 / % possible obs: 99.68 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.39 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1614 / Rpim(I) all: 0.1002 / Rrim(I) all: 0.1904 / Net I/σ(I): 6.88 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 10117 / CC1/2: 0.486 / CC star: 0.809 / Rpim(I) all: 0.6169 / Rrim(I) all: 1.188 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KD2, 8E1C Resolution: 2.4→47.44 Å / SU ML: 0.3079 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3397 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Authors state that the atoms modeled with zero occupancy could not be placed with confidence and were selected for zero-occupancy flagging after manual inspection of the 2Fo-Fc map at a 0.5- ...Details: Authors state that the atoms modeled with zero occupancy could not be placed with confidence and were selected for zero-occupancy flagging after manual inspection of the 2Fo-Fc map at a 0.5-sigma cutoff. Although the correlation is low, residues listed as RSRZ outliers have reasonable concordance with the 2Fo-Fc map, are not rotamer outliers, and are devoid of clashes with neighboring atoms.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.44 Å
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Refine LS restraints |
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LS refinement shell |
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