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Yorodumi- PDB-8gjr: Crystal Structure of Nanobody VHH114 Bound to Its Antigen PA14 Cif -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gjr | ||||||||||||||||||
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Title | Crystal Structure of Nanobody VHH114 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 / CITRATE ANION / CFTR inhibitory factor Function and homology information | ||||||||||||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) Vicugna pacos (alpaca) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 VHH114 Bound to Its Antigen PA14 Cif Authors: Simard, A.R. / Madden, D.R. #1: Journal: Anal Chim Acta / Year: 2019 Title: Nanobody-based binding assay for the discovery of potent inhibitors of CFTR inhibitory factor (Cif). Authors: Vasylieva, N. / Kitamura, S. / Dong, J. / Barnych, B. / Hvorecny, K.L. / Madden, D.R. / Gee, S.J. / Wolan, D.W. / Morisseau, C. / Hammock, B.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gjr.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gjr.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 8gjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gjr_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 8gjr_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 8gjr_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 8gjr_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/8gjr ftp://data.pdbj.org/pub/pdb/validation_reports/gj/8gjr | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33335.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA14_26090 / Plasmid: pET16b / Details (production host): N-terminal 10XHis-SUMO fusion / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3KL26 | ||||
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#2: Antibody | Mass: 13525.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET16b / Details (production host): 10XHis-SUMO fusion / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % / Description: hexagonal rods |
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Crystal grow | Temperature: 292.8 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 13.5 % (w/v) PEG6K, 2.5 % (v/v) ethylene glycol, 100 mM sodium citrate pH 3.5 |
-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-1 / Wavelength: 0.920112 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920112 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→27.62 Å / Num. obs: 50643 / % possible obs: 99.91 % / Redundancy: 20.2 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.03181 / Rrim(I) all: 0.1427 / Net I/σ(I): 16.31 |
Reflection shell | Resolution: 1.85→1.916 Å / Redundancy: 20.8 % / Rmerge(I) obs: 2.404 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 5007 / CC1/2: 0.618 / CC star: 0.874 / Rpim(I) all: 0.539 / Rrim(I) all: 2.465 / % possible all: 99.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→27.62 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.157 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: 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.
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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: 33.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→27.62 Å
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Refine LS restraints |
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LS refinement shell |
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