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- PDB-4ij3: 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: 4ij3 | |||||||||
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Title | Oxidoreductase Fragment of Human QSOX1 in Complex with a FAB Fragment from an Anti- Human QSOX1 Antibody | |||||||||
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![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / antibody binding / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
Function / homology | ![]() flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / FAD binding / platelet alpha granule lumen / Post-translational protein phosphorylation / specific granule lumen ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / FAD binding / platelet alpha granule lumen / Post-translational protein phosphorylation / specific granule lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein folding / tertiary granule lumen / Platelet degranulation / endoplasmic reticulum lumen / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / extracellular space / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Fass, D. / Grossman, I. | |||||||||
![]() | ![]() Title: An Inhibitory Antibody Blocks the First Step in the Dithiol/Disulfide Relay Mechanism of the Enzyme QSOX1. Authors: Grossman, I. / Alon, A. / Ilani, T. / Fass, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.6 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.9 KB | Display | ![]() |
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Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 26986.654 Da / Num. of mol.: 1 / Fragment: Oxidoreductase fragment, UNP RESIDUES 33-272 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Antibody | Mass: 23639.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Antibody | Mass: 23492.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 19% w/v PEG 4000, 0.4 M ammonium phosphate dibasic, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2012 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 38606 / Num. obs: 37560 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 55.29 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 14.35 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 1.96 / Num. unique all: 1769 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q6O, 3OKD Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.72 Å
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