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- PDB-1db2: CRYSTAL STRUCTURE OF NATIVE PLASMINOGEN ACTIVATOR INHIBITOR-1 -

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Basic information

Entry
Database: PDB / ID: 1db2
TitleCRYSTAL STRUCTURE OF NATIVE PLASMINOGEN ACTIVATOR INHIBITOR-1
ComponentsPLASMINOGEN ACTIVATOR INHIBITOR-1
Keywordshydrolase 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 / peptidase inhibitor complex / positive regulation of coagulation / negative regulation of smooth muscle cell migration / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of coagulation / negative regulation of smooth muscle cell migration / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / regulation of signaling receptor activity / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / positive regulation of monocyte chemotaxis / replicative senescence / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / ECM proteoglycans / 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 proteolysis / BMAL1:CLOCK,NPAS2 activates circadian expression / platelet alpha granule lumen / negative regulation of cell migration / positive regulation of interleukin-8 production / serine-type endopeptidase inhibitor activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / positive regulation of inflammatory response / Platelet degranulation / : / cellular response to lipopolysaccharide / protease binding / angiogenesis / defense response to Gram-negative bacterium / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsNar, H. / Bauer, M. / Stassen, J.M. / Lang, D. / Gils, A. / Declerck, P.
CitationJournal: 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
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN ACTIVATOR INHIBITOR-1
B: PLASMINOGEN ACTIVATOR INHIBITOR-1


Theoretical massNumber of molelcules
Total (without water)85,0272
Polymers85,0272
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.600, 92.600, 251.50
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PLASMINOGEN ACTIVATOR INHIBITOR-1


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
1200 mM1reservoirNaCl
210 mMsodium potassium phosphate1reservoir
3protein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1662 -random
Rwork0.255 ---
all-33323 --
obs-31369 94.1 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5887 0 0 0 5887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_deg2.1
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_deg1.7

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