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- PDB-3lw2: Mouse Plasminogen Activator Inhibitor-1 (PAI-1) -

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Basic information

Entry
Database: PDB / ID: 3lw2
TitleMouse Plasminogen Activator Inhibitor-1 (PAI-1)
ComponentsPlasminogen activator inhibitor 1
KeywordsHYDROLASE INHIBITOR / latent mouse plasminogen activator inhibitor-1 (PAI-1) / Glycoprotein / Plasminogen activation
Function / homology
Function and homology information


positive regulation of epithelium regeneration / Dissolution of Fibrin Clot / ECM proteoglycans / positive regulation of leukotriene production involved in inflammatory response / cellular response to xenobiotic stimulus => GO:0071466 / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / positive regulation of coagulation / negative regulation of smooth muscle cell migration / negative regulation of vascular wound healing ...positive regulation of epithelium regeneration / Dissolution of Fibrin Clot / ECM proteoglycans / positive regulation of leukotriene production involved in inflammatory response / cellular response to xenobiotic stimulus => GO:0071466 / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / positive regulation of coagulation / negative regulation of smooth muscle cell migration / negative regulation of vascular wound healing / chromaffin granule / Platelet degranulation / positive regulation of odontoblast differentiation / positive regulation of keratinocyte migration / negative regulation of cell adhesion mediated by integrin / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / female gonad development / positive regulation of calcium ion import / replicative senescence / positive regulation of collagen biosynthetic process / cellular response to interleukin-1 / positive regulation of blood coagulation / regulation of angiogenesis / negative regulation of fibrinolysis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to transforming growth factor beta stimulus / negative regulation of cell migration / positive regulation of interleukin-8 production / placenta development / serine-type endopeptidase inhibitor activity / positive regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / positive regulation of fibroblast proliferation / regulation of cell population proliferation / collagen-containing extracellular matrix / protease binding / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / negative regulation of gene expression / signaling receptor binding / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / cytoplasm
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsDewilde, M. / Van De Craen, B. / Compernolle, G. / Madsen, J.B. / Strelkov, S.V. / Gils, A. / Declerck, P.J.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Subtle structural differences between human and mouse PAI-1 reveal the basis for biochemical differences.
Authors: Dewilde, M. / Van De Craen, B. / Compernolle, G. / Madsen, J.B. / Strelkov, S. / Gils, A. / Declerck, P.J.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,7961
Polymers42,7961
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.900, 62.300, 52.200
Angle α, β, γ (deg.)90.00, 105.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42795.988 Da / Num. of mol.: 1 / Fragment: PAI-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Serpine1, Mr1, Pai1, Planh1 / Plasmid: pIGE20 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P22777
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS CLAIMED AN ERROR IN THE UNP P22777 SEQUENCE AT RESIDUE 253.

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v PEG 3,350, 277 K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0001 Å
DetectorType: Pilatus / Detector: PIXEL / Date: Nov 17, 2007
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.93→39.94 Å / Num. all: 35973 / Num. obs: 34894 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rsym value: 0.068
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.474 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DVN

1dvn


Resolution: 1.93→39.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.648 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21832 1704 5 %RANDOM
Rwork0.18072 ---
obs0.1826 32202 100 %-
all-35973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.314 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.93→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 0 227 3122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9544050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97424.173139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82815538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.771520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7351.51836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36922983
X-RAY DIFFRACTIONr_scbond_it2.01631153
X-RAY DIFFRACTIONr_scangle_it3.2274.51062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.933→1.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 126 -
Rwork0.231 2300 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 22.678 Å / Origin y: -9.759 Å / Origin z: 0.564 Å
111213212223313233
T-0.0474 Å20.0132 Å20.0052 Å2--0.0995 Å20.0099 Å2---0.0389 Å2
L1.0734 °2-0.0453 °2-0.2304 °2-0.43 °20.3669 °2--2.9344 °2
S0.0376 Å °0.064 Å °0.0122 Å °0.0414 Å °-0.0397 Å °-0.01 Å °-0.0492 Å °-0.1973 Å °0.0022 Å °

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