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- PDB-8aon: Oxidoreductase fragment of human QSOX1 in complex with a Fab frag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aon | ||||||
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Title | Oxidoreductase fragment of human QSOX1 in complex with a Fab fragment of a humanized anti-QSOX1 antibody | ||||||
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![]() | IMMUNE SYSTEM / antibody / humanized / Fab / QSOX1 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khmelnitsky, L. / Fass, D. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Reliable energy-based antibody humanization and stabilization Authors: Tennenhouse, A. / Khmelnitsky, L. / Yeshaya, N. / Noronha, A. / Lindzen, M. / Khalaila, R. / Zaretsky, I. / Fridmann Sirkis, Y. / Galon-Wolfenson, Y. / Abramson, J. / Yarden, Y. / Fass, D. / Fleishman, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ij3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27000.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23851.689 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23417.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.36 Å / Num. obs: 102949 / % possible obs: 97 % / Redundancy: 2.7 % / Biso Wilson estimate: 46.08 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.075 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.82 % / Num. unique obs: 3817 / Rpim(I) all: 1.127 / % possible all: 98.55 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4IJ3 Resolution: 2.1→49.36 Å / SU ML: 0.3429 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 31.4747 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 55.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.36 Å
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Refine LS restraints |
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LS refinement shell |
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