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Yorodumi- PDB-6r9z: 3D NMR solution structure of ligand peptide (Ac)EVNPPVP of Pro-Pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r9z | ||||||
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Title | 3D NMR solution structure of ligand peptide (Ac)EVNPPVP of Pro-Pro endopeptidase-1 | ||||||
Components | ACE-GLU-VAL-ASN-PRO-PRO-VAL-PRO-NH2 | ||||||
Keywords | HYDROLASE / synthetic model peptide / Pro-Pro endopeptidase-1 | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Diaz, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Molecular determinants of the mechanism and substrate specificity ofClostridium difficileproline-proline endopeptidase-1. Authors: Pichlo, C. / Juetten, L. / Wojtalla, F. / Schacherl, M. / Diaz, D. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r9z.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r9z.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 6r9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r9z_validation.pdf.gz | 354.6 KB | Display | wwPDB validaton report |
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Full document | 6r9z_full_validation.pdf.gz | 411.5 KB | Display | |
Data in XML | 6r9z_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 6r9z_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/6r9z ftp://data.pdbj.org/pub/pdb/validation_reports/r9/6r9z | HTTPS FTP |
-Related structure data
Related structure data | 6r4wC 6r4xC 6r4yC 6r4zC 6r50C 6r51C 6r52C 6r53C 6r54C 6r55C 6r56C 6r57C 6r58C 6r59C 6r5aC 6r5bC 6r5cC C: citing same article (ref.) |
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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/peptide | Mass: 774.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria) |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 2 mM peptide, 90% H2O/10% D2O / Label: 1H_sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 2 mM / Component: peptide / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 0.175 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |