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- PDB-3cvm: High resolution structure of a stable Plasminogen activator inhib... -

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Basic information

Entry
Database: PDB / ID: 3cvm
TitleHigh resolution structure of a stable Plasminogen activator inhibitor type-1 in its protease cleaved form
ComponentsPlasminogen activator inhibitor 1
KeywordsBLOOD CLOTTING / Plasminogen activator inhibitor type-1 / cleaved serpin / Glycoprotein / Plasminogen activation / Polymorphism / 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 / 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 / angiogenesis / collagen-containing extracellular matrix / 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
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å
AuthorsJensen, J.K. / Gettins, P.G.W.
CitationJournal: Protein Sci. / Year: 2008
Title: High-resolution structure of the stable plasminogen activator inhibitor type-1 variant 14-1B in its proteinase-cleaved form: a new tool for detailed interaction studies and modeling.
Authors: Jensen, J.K. / Gettins, P.G.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 40 PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,V.B.CHEN, : R.M.IMMORMINO,J.J. ... PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,V.B.CHEN, : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL, : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON REFERENCE : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.

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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)88,5552
Polymers88,5552
Non-polymers00
Water14,592810
1
A: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)44,2781
Polymers44,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasminogen activator inhibitor 1


Theoretical massNumber of molelcules
Total (without water)44,2781
Polymers44,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.603, 104.014, 76.426
Angle α, β, γ (deg.)90.00, 101.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44277.672 Da / Num. of mol.: 2 / Mutation: N150H, K154T, Q319L, M354I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG130009 / References: UniProt: P05121
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 4.5M Ammonium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→20 Å / Num. all: 76809 / Num. obs: 75140 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 34.051 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.31
Reflection shellResolution: 2.02→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 26519 / Num. unique all: 8364 / Num. unique obs: 8251 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementStarting model: PDB ENTRY 9PAI

9pai


Resolution: 2.02→19.635 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2255 3 %Random
Rwork0.228 ---
obs0.229 75139 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 6.84 Å2 / Biso mean: 25.49 Å2 / Biso min: 71.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.447 Å2-0 Å214.184 Å2
2---2.9 Å2-0 Å2
3---5.348 Å2
Refinement stepCycle: LAST / Resolution: 2.02→19.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11984 0 0 810 12794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612048
X-RAY DIFFRACTIONf_angle_d0.81321760
X-RAY DIFFRACTIONf_chiral_restr0.063942
X-RAY DIFFRACTIONf_plane_restr0.0041825
X-RAY DIFFRACTIONf_dihedral_angle_d13.4023001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.0640.3381410.2944564470599
2.064-2.1120.3281410.2834543468499
2.112-2.1650.3261420.2724575471799
2.165-2.2230.3381410.2694578471999
2.223-2.2880.3721420.2654573471599
2.288-2.3620.2741420.2614598474099
2.362-2.4460.3491420.2474594473699
2.446-2.5440.3111430.2494614475799
2.544-2.660.3031400.2354543468399
2.66-2.7990.3221420.2324592473498
2.799-2.9740.311400.2364527466797
2.974-3.2030.3111410.234559470098
3.203-3.5240.2721390.2114492463197
3.524-4.030.2371410.1854557469897
4.03-5.0630.211380.1824458459696
5.063-19.6360.2551400.2174517465795

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