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- PDB-3q02: Crystal structure of plasminogen activator inhibitor-1 in a metas... -

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Basic information

Entry
Database: PDB / ID: 3q02
TitleCrystal structure of plasminogen activator inhibitor-1 in a metastable active conformation.
ComponentsPlasminogen activator inhibitor 1
KeywordsHYDROLASE 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 / 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 receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / Platelet degranulation / cellular response to lipopolysaccharide / angiogenesis / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / protease binding / 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 / Resolution: 2.3 Å
AuthorsJensen, J.K. / Morth, J.P.
CitationJournal: 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
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 7, 2011Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen activator inhibitor 1
B: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8247
Polymers85,5602
Non-polymers2645
Water2,342130
1
A: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8152
Polymers42,7801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0085
Polymers42,7801
Non-polymers2284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-90 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.438, 67.172, 90.357
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasminogen activator inhibitor 1 / PAI / PAI-1 / Endothelial plasminogen activator inhibitor / Serpin E1


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 ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.39 Å / Redundancy: 4.62 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.706 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVM

1dvm


Resolution: 2.3→24.943 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 2024 5 %5% random selection
Rwork0.1931 ---
obs0.1954 40487 98.73 %-
all-41055 --
Solvent computationShrinkage 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
Baniso -1Baniso -2Baniso -3
1-2.263 Å2-0 Å210.9255 Å2
2--3.2622 Å20 Å2
3----5.5252 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5764 0 8 130 5902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075913
X-RAY DIFFRACTIONf_angle_d1.0268010
X-RAY DIFFRACTIONf_dihedral_angle_d15.6362190
X-RAY DIFFRACTIONf_chiral_restr0.07892
X-RAY DIFFRACTIONf_plane_restr0.0041035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.31971410.27052677X-RAY DIFFRACTION97
2.3575-2.42120.29221450.26492745X-RAY DIFFRACTION99
2.4212-2.49240.36441430.26142742X-RAY DIFFRACTION98
2.4924-2.57280.32791390.26862659X-RAY DIFFRACTION96
2.5728-2.66460.33591440.26432727X-RAY DIFFRACTION99
2.6646-2.77120.33171460.24682773X-RAY DIFFRACTION100
2.7712-2.89710.3261450.23912752X-RAY DIFFRACTION100
2.8971-3.04960.28941450.22492756X-RAY DIFFRACTION99
3.0496-3.24030.27211440.21772739X-RAY DIFFRACTION99
3.2403-3.48990.24231440.20612728X-RAY DIFFRACTION98
3.4899-3.83990.23641460.1862772X-RAY DIFFRACTION100
3.8399-4.39290.18961470.1632792X-RAY DIFFRACTION99
4.3929-5.52470.1951450.15332762X-RAY DIFFRACTION98
5.5247-24.94470.18671500.16032839X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45791.0486-0.72993.2858-2.89964.46890.10710.04680.17230.55040.32710.2779-0.6532-0.1433-0.38830.36290.03180.07240.2279-0.02590.327753.17229.7569-2.3815
22.605-1.1803-1.65421.6984-1.84396.82061.41510.26651.40510.70760.50460.0814-3.5806-0.7967-2.01552.38630.60881.39920.42030.33561.266139.316141.090617.4875
32.77480.5807-0.75631.8061-0.1921.895-0.1728-0.3985-0.02150.14340.0812-0.14980.22760.29840.08270.32160.1342-0.01510.3102-0.00720.183945.59391.675633.1365
40.19410.33620.05710.6111-0.0060.3772-0.2122-0.0786-0.4134-0.16540.236-0.61390.15210.31630.02440.29630.19150.03060.958-0.10170.887270.695-2.340824.3539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A (resid 4:176 or resid 207:379)
2X-RAY DIFFRACTION2chain A resid 177:206
3X-RAY DIFFRACTION3chain B (resid 1:176 or resid 207:379)
4X-RAY DIFFRACTION4chain B resid 177:206

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