+Open data
-Basic information
Entry | Database: PDB / ID: 1db2 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF NATIVE PLASMINOGEN ACTIVATOR INHIBITOR-1 | ||||||
Components | PLASMINOGEN ACTIVATOR INHIBITOR-1 | ||||||
Keywords | hydrolase inhibitor / NATIVE SERPIN | ||||||
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 / Resolution: 2.7 Å | ||||||
Authors | Nar, H. / Bauer, M. / Stassen, J.M. / Lang, D. / Gils, A. / Declerck, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Plasminogen activator inhibitor 1. Structure of the native serpin, comparison to its other conformers and implications for serpin inactivation. Authors: Nar, H. / Bauer, M. / Stassen, J.M. / Lang, D. / Gils, A. / Declerck, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1db2.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1db2.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 1db2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/1db2 ftp://data.pdbj.org/pub/pdb/validation_reports/db/1db2 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42513.738 Da / Num. of mol.: 2 / Mutation: N150H, K154T, Q301P, Q319L, M354I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Tissue fraction: PLASMA / Production host: Escherichia coli (E. coli) / References: UniProt: P05121 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: sodium chloride, sodium/potassium phosphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9057 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9057 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. all: 706774 / Num. obs: 42076 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 16.8 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.55→2.59 Å / Rmerge(I) obs: 0.551 / % possible all: 78.3 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 100 Å / Num. obs: 35572 / % possible obs: 97.8 % / Num. measured all: 603807 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.75 Å / % possible obs: 90.1 % / Rmerge(I) obs: 0.383 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.7→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: THE EXPERIMENTAL DATA SET IS PARTIALLY MEROHEDRALLY TWINNED WITH A TWINNING INDEX OF 0.28. THE STRUCTURE WAS REFINED AGAINST DETWINNED DATA.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 / Num. reflection Rfree: 1954 / Rfactor obs: 0.255 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|