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- PDB-6bzl: Solution structure of VEK75 -

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Basic information

Entry
Database: PDB / ID: 6bzl
TitleSolution structure of VEK75
ComponentsM protein
KeywordsPROTEIN BINDING / Plasminogen binding peptide
Function / homologyPlasminogen 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 / extracellular region / M protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsQiu, C. / Yuan, Y. / Castellino, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL013423 United States
Citation
Journal: J.Struct.Biol. / Year: 2018
Title: Contributions of different modules of the plasminogen-binding Streptococcus pyogenes M-protein that mediate its functional dimerization.
Authors: Qiu, C. / Yuan, Y. / Zajicek, J. / Liang, Z. / Balsara, R.D. / Brito-Robionson, T. / Lee, S.W. / Ploplis, V.A. / Castellino, F.J.
#1: Journal: To Be Published
Title: Structure of PAM
Authors: Qiu, C. / Yuan, Y. / Castellino, F.J.
History
DepositionDec 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 31, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)9,1411
Polymers9,1411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8410 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein M protein / VEK75


Mass: 9141.062 Da / Num. of mol.: 1 / Fragment: UNP residues 88-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: AP53 / Plasmid: pET15b / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q6V4L8

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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 HNCA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D C(CO)NH
171isotropic13D H(CCO)NH
181isotropic13D HBHA(CO)NH
191isotropic13D NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 20 mM [U-99% 2H] BisTris-d19, 1 mM DSS, 1 mM sodium azide, 1 mM EDTA, 90% H2O/10% D2O
Details: 1 mM 15N, 13C-labeled VEK75 / Label: 15N, 13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMBisTris-d19[U-99% 2H]1
1 mMDSSnatural abundance1
1 mMsodium azidenatural abundance1
1 mMEDTAnatural 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 II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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