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Yorodumi- PDB-3q02: Crystal structure of plasminogen activator inhibitor-1 in a metas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q02 | ||||||
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Title | Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. | ||||||
Components | Plasminogen activator inhibitor 1 | ||||||
Keywords | HYDROLASE INHIBITOR / PAI-1 / active serpin / serine protease inhibitor / metastable conformation | ||||||
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 endopeptidase activity ...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 endopeptidase activity / negative regulation of plasminogen activation / negative regulation of blood coagulation / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / Dissolution of Fibrin Clot / serine protease inhibitor complex / 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 / fibrinolysis / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / negative regulation of cell migration / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / serine-type endopeptidase inhibitor activity / Platelet degranulation / protease binding / cellular response to lipopolysaccharide / angiogenesis / collagen-containing extracellular matrix / 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: 2.3 Å | ||||||
Authors | Jensen, J.K. / Morth, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure of plasminogen activator inhibitor-1 in an active conformation with normal thermodynamic stability. Authors: Jensen, J.K. / Thompson, L.C. / Bucci, J.C. / Nissen, P. / Gettins, P.G. / Peterson, C.B. / Andreasen, P.A. / Morth, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q02.cif.gz | 305 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q02.ent.gz | 249.3 KB | Display | PDB format |
PDBx/mmJSON format | 3q02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q02_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 3q02_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 3q02_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3q02_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/3q02 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/3q02 | HTTPS FTP |
-Related structure data
Related structure data | 3q03C 1dvmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42780.031 Da / Num. of mol.: 2 / Mutation: W175F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAI1, PLANH1, SERPINE1 / Plasmid: pET-24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta 2 pLysS / References: UniProt: P05121 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 41055 / Num. obs: 40531 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 4.62 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.706 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DVM Resolution: 2.3→24.943 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 28.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.837 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→24.943 Å
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Refine LS restraints |
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LS refinement shell |
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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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