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- PDB-5v4u: Solution structure of VKK38 bound to plasminogen kringle 2 -

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Basic information

Entry
Database: PDB / ID: 5v4u
TitleSolution structure of VKK38 bound to plasminogen kringle 2
ComponentsM protein
KeywordsBLOOD CLOTTING / PROTEIN/PEPTIDE
Function / homology
Function and homology information


cell wall / membrane => GO:0016020 / extracellular region
Similarity search - Function
M protein repeat / M protein repeat / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / : / M protein-type anchor domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
M protein / M protein type 52
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, Y. / Castellino, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL013423 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Conformationally organized lysine isosteres in Streptococcus pyogenes M protein mediate direct high-affinity binding to human plasminogen.
Authors: Yuan, Y. / Zajicek, J. / Qiu, C. / Chandrahas, V. / Lee, S.W. / Ploplis, V.A. / Castellino, F.J.
History
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M protein


Theoretical massNumber of molelcules
Total (without water)4,8921
Polymers4,8921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide M protein


Mass: 4892.360 Da / Num. of mol.: 1 / Fragment: UNP residues 60-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: emm / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059T9N2, UniProt: Q54839*PLUS

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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 HNCO
131isotropic13D C(CO)NH
141isotropic13D CBCA(CO)NH
151isotropic13D HNCA
161isotropic12D 1H-13C HSQC aromatic
171isotropic13D 15N HSQC-NOESY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] VKK38, 2.5 mM Kringle2, 20 mM [U-100% 2H] BisTris-d19, 0.2 mM DSS, 2 mM EDTA, 3 mM sodium azide, 95% H2O/5% D2O
Label: 15N, 13C / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMVKK38[U-13C; U-15N]1
2.5 mMKringle2natural abundance1
20 mMBisTris-d19[U-100% 2H]1
0.2 mMDSSnatural abundance1
2 mMEDTAnatural abundance1
3 mMsodium azidenatural abundance1
Sample conditionsIonic strength: 20 mM / Label: condition_1 / pH: 6.7 / 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 Biospinchemical shift assignment
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOS-NCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospinpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 20

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