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- PDB-1l4d: CRYSTAL STRUCTURE OF MICROPLASMINOGEN-STREPTOKINASE ALPHA DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1l4d
TitleCRYSTAL STRUCTURE OF MICROPLASMINOGEN-STREPTOKINASE ALPHA DOMAIN COMPLEX
Components
  • PLASMINOGEN
  • STREPTOKINASE
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / streptokinase / plasminogen / protein complex / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / protein processing / 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 / endopeptidase activity / blood microparticle / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #180 / Streptokinase / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain ...Ubiquitin-like (UB roll) - #180 / Streptokinase / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / 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 / Ubiquitin-like (UB roll) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen / Streptokinase C
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWakeham, N. / Terzyan, S. / Zhai, P. / Loy, J.A. / Tang, J. / Zhang, X.C.
CitationJournal: PROTEIN ENG. / Year: 2002
Title: Effects of deletion of streptokinase residues 48-59 on plasminogen activation
Authors: Wakeham, N. / Terzyan, S. / Zhai, P. / Loy, J.A. / Tang, J. / Zhang, X.C.
History
DepositionMar 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMINOGEN
B: STREPTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8964
Polymers40,7042
Non-polymers1922
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-27 kcal/mol
Surface area16870 Å2
MethodPISA
2
A: PLASMINOGEN
B: STREPTOKINASE
hetero molecules

A: PLASMINOGEN
B: STREPTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7938
Polymers81,4094
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7960 Å2
ΔGint-91 kcal/mol
Surface area29110 Å2
MethodPISA
3
A: PLASMINOGEN
hetero molecules

B: STREPTOKINASE


Theoretical massNumber of molelcules
Total (without water)40,8964
Polymers40,7042
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2340 Å2
ΔGint-35 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.449, 94.177, 126.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21B-181-

HOH

DetailsContains one molecule of microplasminogen and one molecule of streptokinase alpha domain

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Components

#1: Protein PLASMINOGEN


Mass: 27248.326 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, Residues 543-791 / Mutation: S741A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00747, plasmin
#2: Protein STREPTOKINASE


Mass: 13455.990 Da / Num. of mol.: 1 / Fragment: ALPHA DOMAIN, Residues 14-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Species: Streptococcus dysgalactiae / Strain: subsp. equisimilis / Plasmid: PET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00779
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Li2SO4, Hepes, Mg Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mg/mlSKalpha1drop
220 mMTris-HCl1droppH8.0
30.4 Murea1drop
416 mg/mluPgS741A1drop
520 mMHEPES1droppH7.5
60.4 Murea1drop
70.02 %(w/v)NaN31drop
81.0 M1reservoirLi2SO4
950 mMHEPES1reservoirpH7.0
1010 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 9, 2001 / Details: Osmic Confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→23.61 Å / Num. all: 16883 / Num. obs: 16883 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 32.36 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.48
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1803 / % possible all: 64.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. obs: 16982
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 64.7 % / Num. unique obs: 1167 / Rmerge(I) obs: 0.47

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDJ

1ddj


Resolution: 2.3→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1060 7 %Random
Rwork0.206 ---
all-15443 --
obs-15443 --
Solvent computationBsol: 43.8518 Å2 / ksol: 0.388818 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.33 Å20 Å20 Å2
2---12.122 Å20 Å2
3---4.792 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 10 213 3016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.73
LS refinement shellHighest resolution: 2.3 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0096

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