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Yorodumi- PDB-6i8s: Discovery and characterisation of an antibody that selectively mo... -
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-Basic information
Entry | Database: PDB / ID: 6i8s | ||||||
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Title | Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1 | ||||||
Components |
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Keywords | BLOOD CLOTTING / SERPIN / PLASMINOGEN ACTIVATOR INHIBITOR-1 / PAI-1 / ANTIBODY / FAB | ||||||
Function / homology | Function and homology information positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of blood coagulation ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of blood coagulation / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / regulation of signaling receptor activity / Dissolution of Fibrin Clot / positive regulation of monocyte chemotaxis / replicative senescence / ECM proteoglycans / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / serine protease inhibitor complex / fibrinolysis / negative regulation of cell migration / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Platelet degranulation / collagen-containing extracellular matrix / angiogenesis / cellular response to lipopolysaccharide / protease binding / defense response to Gram-negative bacterium / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Vousden, K.A. / Lundqvist, T. / Popovic, B. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1. Authors: Vousden, K.A. / Lundqvist, T. / Popovic, B. / Naiman, B. / Carruthers, A.M. / Newton, P. / Johnson, D.J.D. / Pomowski, A. / Wilkinson, T. / Dufner, P. / de Mendez, I. / Mallinder, P.R. / ...Authors: Vousden, K.A. / Lundqvist, T. / Popovic, B. / Naiman, B. / Carruthers, A.M. / Newton, P. / Johnson, D.J.D. / Pomowski, A. / Wilkinson, T. / Dufner, P. / de Mendez, I. / Mallinder, P.R. / Murray, C. / Strain, M. / Connor, J. / Murray, L.A. / Sleeman, M.A. / Lowe, D.C. / Huntington, J.A. / Vaughan, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i8s.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6i8s.ent.gz | 1023.4 KB | Display | PDB format |
PDBx/mmJSON format | 6i8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/6i8s ftp://data.pdbj.org/pub/pdb/validation_reports/i8/6i8s | HTTPS FTP |
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-Related structure data
Related structure data | 4g8rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42782.023 Da / Num. of mol.: 4 / Mutation: YES [N150H, K154T, Q319L, M354I,] Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05121 #2: Antibody | Mass: 23719.564 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 23439.076 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: ARTIFICIALLY MADE ANTIBODY / Production host: Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | Sequence details | MUTATIONS N150H, K154T, Q319L, M354I | |
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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: 2.68 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15 MM AMMONIUM ACETATE PH 7.4, 8-10 % PEG 8000, 0.2 M LICL AND 20 % ETHYLENE GLYCOL PH range: 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→14.99 Å / Num. obs: 86268 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 86.49 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.6 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G8R Resolution: 2.9→14.99 Å / Cor.coef. Fo:Fc: 0.8908 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.36
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Displacement parameters | Biso mean: 63.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.449 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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