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- PDB-3eox: High quality structure of cleaved PAI-1-stab -

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Basic information

Entry
Database: PDB / ID: 3eox
TitleHigh quality structure of cleaved PAI-1-stab
ComponentsPlasminogen activator inhibitor 1
KeywordsBLOOD CLOTTING / cleaved plasminogen activator inhibitor-1 / PAI-1 / Serpin / Stabilized / Glycoprotein / Plasminogen activation / Protease inhibitor / Secreted / Serine protease inhibitor
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 / 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 / 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 / serine-type endopeptidase inhibitor activity / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / 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
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsDewilde, M. / Declerck, P.J. / Rabijns, A. / Strelkov, S.V.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: High quality structure of cleaved PAI-1-stab.
Authors: Dewilde, M. / Strelkov, S.V. / Rabijns, A. / Declerck, P.J.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 10, 2021Group: Advisory / Data collection / Database references
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)42,7511
Polymers42,7511
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.174, 71.174, 141.664
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Plasminogen activator inhibitor 1 / PAI-1 / PAI / Endothelial plasminogen activator inhibitor


Mass: 42751.008 Da / Num. of mol.: 1 / Fragment: PAI-1 / Mutation: N150H, K154T, Q301P, Q319L, M354I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Plasmid: pIGE20 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P05121
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5M lithium sulphate monohydrate, 15% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8084 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2006
RadiationMonochromator: Si 111 horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8084 Å / Relative weight: 1
ReflectionResolution: 2.61→19.73 Å / Num. obs: 12280

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
detectorsoftwaredata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 9PAI

9pai


Resolution: 2.61→19.73 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0 / SU B: 23.519 / SU ML: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 603 4.9 %RANDOM
Rwork0.201 ---
all0.204 12818 --
obs0.204 12280 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.52 Å2 / Biso mean: 5.975 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.61→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 0 123 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0223030
X-RAY DIFFRACTIONr_angle_refined_deg0.7921.9534116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6915371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36323.796137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4131517
X-RAY DIFFRACTIONr_chiral_restr0.0550.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212289
X-RAY DIFFRACTIONr_mcbond_it0.1811.51855
X-RAY DIFFRACTIONr_mcangle_it0.35923020
X-RAY DIFFRACTIONr_scbond_it0.54431175
X-RAY DIFFRACTIONr_scangle_it0.9774.51094
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 50 -
Rwork0.246 806 -
all-856 -
obs--93.45 %
Refinement TLS params.Method: refined / Origin x: 17.094 Å / Origin y: -27.439 Å / Origin z: 22.082 Å
111213212223313233
T0.0785 Å2-0.0038 Å20.0146 Å2-0.103 Å2-0.006 Å2--0.1875 Å2
L1.5702 °2-0.2298 °2-0.0363 °2-1.8915 °2-0.6317 °2--1.2076 °2
S0.0373 Å °0.0434 Å °0.1167 Å °-0.0131 Å °-0.013 Å °0.0056 Å °-0.0621 Å °-0.0163 Å °-0.0243 Å °

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