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- PDB-7e50: Crystal structure of human microplasmin in complex with kazal-typ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+50
TitleCrystal structure of human microplasmin in complex with kazal-type inhibitor AaTI
Components
  • AAEL006007-PA
  • Plasminogen
KeywordsHYDROLASE / Plasmin
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / myoblast differentiation / negative regulation of cell-substrate adhesion / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / kinase binding / Schaffer collateral - CA1 synapse / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / divergent subfamily of APPLE domains / : / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / PAN/Apple domain profile. ...Peptidase S1A, plasmin / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / divergent subfamily of APPLE domains / : / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Plasminogen / Kazal domain-containing peptide
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsVarsha, A.W. / Jobichen, C. / Mok, Y.K.
CitationJournal: Protein Sci. / Year: 2022
Title: Crystal structure of Aedes aegypti trypsin inhibitor in complex with mu-plasmin reveals role for scaffold stability in Kazal-type serine protease inhibitor.
Authors: Walvekar, V.A. / Ramesh, K. / Jobichen, C. / Kannan, M. / Sivaraman, J. / Kini, R.M. / Mok, Y.K.
History
DepositionFeb 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAEL006007-PA
B: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8336
Polymers36,6722
Non-polymers1614
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-42 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.895, 86.044, 50.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AAEL006007-PA / Kazal domain-containing peptide


Mass: 8820.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL006007
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q1HRB8
#2: Protein Plasminogen / MicroPlasminogen


Mass: 27850.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00747, plasmin
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium formate, 20 % polyethylene glycol 3350 pH 6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→44.72 Å / Num. obs: 28769 / % possible obs: 99.6 % / Redundancy: 12.4 % / Rpim(I) all: 0.057 / Net I/σ(I): 7.8
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 1736 / Rpim(I) all: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D3X

6d3x


Resolution: 1.95→19.78 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 1742 7.94 %
Rwork0.218 20207 -
obs0.2224 21949 92.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.1 Å2 / Biso mean: 49.15 Å2 / Biso min: 22.64 Å2
Refinement stepCycle: final / Resolution: 1.95→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 9 138 2401
Biso mean--41.38 44.52 -
Num. residues----300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.010.34081530.32531775192899
2.01-2.050.33391100.31751283139398
2.08-2.150.37291370.29721586172398
2.15-2.230.32511520.28271767191999
2.23-2.330.34311130.27391312142572
2.33-2.460.29461540.25971784193899
2.46-2.610.30511560.247918001956100
2.61-2.810.32251550.242518031958100
2.81-3.090.3121560.241318121968100
3.09-3.540.28111490.22071711186093
3.54-4.450.23251400.17721632177288
4.45-19.780.21921670.168119422109100
Refinement TLS params.Method: refined / Origin x: 15.4138 Å / Origin y: 23.1472 Å / Origin z: 11.1548 Å
111213212223313233
T0.3245 Å20.0346 Å2-0.0616 Å2-0.2509 Å2-0.0299 Å2--0.269 Å2
L1.6651 °2-0.4169 °20.3364 °2-4.4866 °2-1.1558 °2--1.4948 °2
S-0.1008 Å °-0.2091 Å °0.1221 Å °0.903 Å °0.1547 Å °-0.1605 Å °-0.194 Å °0.0257 Å °-0.0674 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 56
2X-RAY DIFFRACTION1allB545 - 791
3X-RAY DIFFRACTION1allB801
4X-RAY DIFFRACTION1allC1 - 4
5X-RAY DIFFRACTION1allS1 - 164

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