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- PDB-6oq9: Solution structure of VEK50 in the bound form with plasminogen kr... -

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Basic information

Entry
Database: PDB / ID: 6oq9
TitleSolution structure of VEK50 in the bound form with plasminogen kringle 2
ComponentsPlasminogen-binding group A streptococcal M-like protein PAM
KeywordsPROTEIN BINDING / Plasminogen binding peptide / blood clotting
Function / homology
Function and homology information


plasminogen activation / extracellular region
Similarity search - Function
Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / YSIRK Gram-positive signal peptide
Similarity search - Domain/homology
Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, Y. / Castellino, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HL013423 United States
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes.
Authors: Yuan, Y. / Ayinuola, Y.A. / Singh, D. / Ayinuola, O. / Mayfield, J.A. / Quek, A. / Whisstock, J.C. / Law, R.H.P. / Lee, S.W. / Ploplis, V.A. / Castellino, F.J.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nmr_spectrometer.model
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasminogen-binding group A streptococcal M-like protein PAM


Theoretical massNumber of molelcules
Total (without water)6,1741
Polymers6,1741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5080 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Plasminogen-binding group A streptococcal M-like protein PAM


Mass: 6173.791 Da / Num. of mol.: 1 / Fragment: residues 85-133
Source method: isolated from a genetically manipulated source
Details: AP53 / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: pam, emm / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P49054

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D C(CO)NH
141isotropic13D HNCO
151isotropic13D HNCA
161isotropic13D HN(CA)CB
171isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] VEK50, 1.5 mM Kringle 2, 2 ug/mL DSS, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL sodium azide, 93% H2O/7% D2O
Details: 13C, 15N-labeled VEK50 with unlabeled Kringle 2 at molar ratio of 1:2 in 20 mM Bis-Tris-d19 buffer at pH 6.8
Label: 13C, 15N_sample / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVEK50[U-99% 13C; U-99% 15N]1
1.5 mMKringle 2natural abundance1
2 ug/mLDSSnatural abundance1
20 mMBis-Tris-d19[U-2H]1
2 ug/mLsodium azidenatural abundance1
Sample conditionsIonic strength: 20 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 15

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