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- PDB-1i5k: STRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 D... -

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Basic information

Entry
Database: PDB / ID: 1i5k
TitleSTRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 DOMAIN OF HUMAN PLASMINOGEN TO AN INTERNAL PEPTIDE FROM A GROUP A STREPTOCOCCAL SURFACE PROTEIN
Components
  • M PROTEIN
  • PLASMINOGENPlasmin
KeywordsBLOOD CLOTTING / Human Plasminogen Kringle-2 / Kringles / VEK-30
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / plasminogen activation / 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 / Schaffer collateral - CA1 synapse / kinase binding / 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 / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Streptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain ...Streptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / YSIRK Gram-positive signal peptide / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Plasminogen / Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRios-Steiner, J.L. / Schenone, M. / Mochalkin, I. / Tulinsky, A. / Castellino, F.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein.
Authors: Rios-Steiner, J.L. / Schenone, M. / Mochalkin, I. / Tulinsky, A. / Castellino, F.J.
#1: Journal: Biochemistry / Year: 1998
Title: Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen.
Authors: Chang, Y. / Mochalkin, I. / McCance, S.G. / Cheng, B. / Tulinsky, A. / Castellino, F.J.
#2: Journal: Biochemistry / Year: 1991
Title: The refined structure of the epsilon-aminocaproic acid complex of human plasminogen kringle 4.
Authors: Wu, T.P. / Padmanabhan, K. / Tulinsky, A. / Mulichak, A.M.
#3: Journal: J.Biol.Chem. / Year: 1998
Title: Kringle 2 mediates high affinity binding of plasminogen to an internal sequence in streptococcal surface protein PAM.
Authors: Wistedt, A.C. / Kotarsky, H. / Marti, D. / Ringdahl, U. / Castellino, F.J. / Schaller, J. / Sjobring, U.
#4: Journal: J.Biol.Chem. / Year: 1999
Title: Enhancement trough mutagenesis of the binding of the isolated kringle 2 domain of human plasminogen to omega-amino acid ligands and to an internal sequence of a Streptococcal surface protein.
Authors: Nilsen, S.L. / Prorok, M. / Castellino, F.J.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 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 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN
B: PLASMINOGEN
C: M PROTEIN
D: M PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8204
Polymers26,8204
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.98, 91.98, 151.779
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

DetailsThe assembly in the assymetric unit constitutes a dimer of the monomeric complex of a Kringle-2:vek30 complex.

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Components

#1: Protein PLASMINOGEN / Plasmin


Mass: 9774.923 Da / Num. of mol.: 2 / Fragment: MODIFIED RECOMBINANT KRINGLE-2 DOMAIN / Mutation: C4G/E56D/L72Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P00747, plasmin
#2: Protein/peptide M PROTEIN


Mass: 3635.021 Da / Num. of mol.: 2 / Fragment: VEK-30 (30 RESIDUE INTERNAL PEPTIDE) / Source method: obtained synthetically
Details: VEK-30 was synthesized by automated solid phase peptide synthesis
References: UniProt: P49054
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23%(w/v) PEG 3350, 0.1 M Mes, 0.2 M Li2SO4, 2mM CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 %(w/v)PEG33501reservoir
20.1 MMES1reservoir
30.2 M1reservoirLi2SO4
42 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.039 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2000
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 74852 / Num. obs: 73280 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11063 / % possible all: 84.3
Reflection
*PLUS
Num. obs: 11063 / Num. measured all: 74852
Reflection shell
*PLUS
% possible obs: 84.3 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Using K4 Pg (PDB entry 1PK4)

1pk4


Resolution: 2.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 477 -Random
Rwork0.195 ---
all-9144 --
obs-8667 87.2 %-
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 0 133 1870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONB rmsd for bonded main chain1.2
X-RAY DIFFRACTIONB rmsd for side chain atoms1.8
X-RAY DIFFRACTIONB rmsd for angle main chain2.1
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 1.5 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_mcbond_it1.2
X-RAY DIFFRACTIONc_scbond_it1.8
X-RAY DIFFRACTIONc_mcangle_it2.1
X-RAY DIFFRACTIONc_scangle_it3

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