+Open data
-Basic information
Entry | Database: PDB / ID: 4ouo | ||||||
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Title | anti-Bla g 1 scFv | ||||||
Components | anti Bla g 1 scFv | ||||||
Keywords | IMMUNE SYSTEM / cockroach allergen / IgG / scFv antibody fragment / Bla g 1 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mueller, G.A. / Ankney, J.A. / Glesner, J. / Khurana, T. / Edwards, L.L. / Pedersen, L.C. / Perera, L. / Slater, J.E. / Pomes, A. / London, R.E. | ||||||
Citation | Journal: Mol.Immunol. / Year: 2014 Title: Characterization of an anti-Bla g 1 scFv: Epitope mapping and cross-reactivity. Authors: Mueller, G.A. / Ankney, J.A. / Glesner, J. / Khurana, T. / Edwards, L.L. / Pedersen, L.C. / Perera, L. / Slater, J.E. / Pomes, A. / London, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ouo.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ouo.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ouo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/4ouo ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4ouo | HTTPS FTP |
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-Related structure data
Related structure data | 3ux9S 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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Details | ScFv biological unit is a monomer but due to a too short linker between the two IgG domains, the N-terminal domain of one molecule forms the biological scFv structure with the C-terminal domain of another molecule (and vise-versa) that is related by a 180 degree rotation. |
-Components
#1: Antibody | Mass: 24524.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 46.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8M Ammonium Sulfate, 100mM NaCl, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2012 |
Radiation | Monochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 19780 / Num. obs: 19780 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.45 Å2 / Rsym value: 0.048 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 758 / Rsym value: 0.176 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UX9 Resolution: 1.8→29.654 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.25 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.654 Å
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Refine LS restraints |
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LS refinement shell |
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