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Yorodumi- PDB-6oq9: Solution structure of VEK50 in the bound form with plasminogen kr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oq9 | ||||||
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Title | Solution structure of VEK50 in the bound form with plasminogen kringle 2 | ||||||
Components | Plasminogen-binding group A streptococcal M-like protein PAM | ||||||
Keywords | PROTEIN BINDING / Plasminogen binding peptide / blood clotting | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Yuan, Y. / Castellino, F.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oq9.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oq9.ent.gz | 211.5 KB | Display | PDB format |
PDBx/mmJSON format | 6oq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oq9_validation.pdf.gz | 527.2 KB | Display | wwPDB validaton report |
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Full document | 6oq9_full_validation.pdf.gz | 701.3 KB | Display | |
Data in XML | 6oq9_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 6oq9_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/6oq9 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/6oq9 | HTTPS FTP |
-Related structure data
Related structure data | 6okwC 6okxC 6okyC 6oqjC 6oqkC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 15 |