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- PDB-6r9z: 3D NMR solution structure of ligand peptide (Ac)EVNPPVP of Pro-Pr... -

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Basic information

Entry
Database: PDB / ID: 6r9z
Title3D NMR solution structure of ligand peptide (Ac)EVNPPVP of Pro-Pro endopeptidase-1
ComponentsACE-GLU-VAL-ASN-PRO-PRO-VAL-PRO-NH2
KeywordsHYDROLASE / synthetic model peptide / Pro-Pro endopeptidase-1
Biological speciesClostridioides difficile (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDiaz, D.
CitationJournal: 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
DepositionApr 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 7, 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 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ACE-GLU-VAL-ASN-PRO-PRO-VAL-PRO-NH2


Theoretical massNumber of molelcules
Total (without water)7751
Polymers7751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area210 Å2
ΔGint-0 kcal/mol
Surface area1080 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ACE-GLU-VAL-ASN-PRO-PRO-VAL-PRO-NH2


Mass: 774.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 2 mM peptide, 90% H2O/10% D2O / Label: 1H_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.175 M / Label: conditions_1 / pH: 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: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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