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- PDB-1lj5: 1.8A Resolution Structure of Latent Plasminogen Activator Inhibit... -

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Basic information

Entry
Database: PDB / ID: 1lj5
Title1.8A Resolution Structure of Latent Plasminogen Activator Inhibitor-1(PAI-1)
ComponentsPLASMINOGEN ACTIVATOR INHIBITOR-1
KeywordsBLOOD CLOTTING / beta-barrell
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
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
ACETIC ACID / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStein, P.E. / Baek, K.
History
DepositionApr 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1926
Polymers42,8191
Non-polymers3735
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.574, 46.885, 63.048
Angle α, β, γ (deg.)90.00, 106.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PLASMINOGEN ACTIVATOR INHIBITOR-1 / / PAI-1 / Endothelial plasminogen activator inhibitor / PAI


Mass: 42819.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1 / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P05121
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, sodium acetate trihydrate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationMonochromator: cooled liquid gallium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→27.7 Å / Num. all: 37680 / Num. obs: 37614 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.1 % / Biso Wilson estimate: 15.4 Å2 / Limit h max: 83 / Limit h min: -86 / Limit k max: 26 / Limit k min: -86 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 1705578.33 / Observed criterion F min: 6.7 / Rmerge(I) obs: 0.126 / Rsym value: 0.105 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.1 / Num. unique all: 3745 / Rsym value: 0.669 / % possible all: 63.4

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1dvn

1dvn


Resolution: 1.8→27.7 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1885 5 %random
Rwork0.198 ---
all-40961 --
obs-37614 91.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 72.7301 Å2 / ksol: 0.384043 e/Å3
Displacement parametersBiso max: 95.71 Å2 / Biso mean: 22.97 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å21.88 Å2
2--4.4 Å20 Å2
3----6.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 16 327 3356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.3361593.10.34229970.0275095315661.9
1.88-1.980.2582354.60.2637580.0175072399378.7
1.98-2.110.2162384.70.21546470.0145097488595.8
2.11-2.270.2082605.10.20348160.0135096507699.6
2.27-2.50.1872514.90.18447980.0125081504999.4
2.5-2.860.1862114.10.18549000.0135135511199.5
2.86-3.60.1782524.90.17748680.0115148512099.5
3.6-27.70.1912795.30.19149450.0115275522499
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3acy_xplor.paramacy_xplor.top
X-RAY DIFFRACTION4dms_xplor.paramdms_xplor.top

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