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- PDB-2m7i: Solution structure of a Beta-Hairpin Peptidomimetic antibiotic th... -

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Basic information

Entry
Database: PDB / ID: 2m7i
TitleSolution structure of a Beta-Hairpin Peptidomimetic antibiotic that targets LptD in Pseudomonas sp.
ComponentsBeta-Hairpin Peptidomimetic antibiotic TWL(DAB)(ORN)(DLY)RW(ORN)(DAB)AK(DPR)P
KeywordsANTIBIOTIC / Peptidomimetics / beta-hairpin
Function / homologyBeta-Hairpin Peptidomimetic antibiotic TWL(DAB)(ORN)(DLY)RW(ORN)(DAB)AK(DPR)P
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsMoehle, K. / Schmidt, J. / Robinson, J.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Structural studies of beta-hairpin peptidomimetic antibiotics that target LptD in Pseudomonas sp.
Authors: Schmidt, J. / Patora-Komisarska, K. / Moehle, K. / Obrecht, D. / Robinson, J.A.
History
DepositionApr 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-Hairpin Peptidomimetic antibiotic TWL(DAB)(ORN)(DLY)RW(ORN)(DAB)AK(DPR)P


Theoretical massNumber of molelcules
Total (without water)1,7131
Polymers1,7131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 Beta-Hairpin Peptidomimetic antibiotic TWL(DAB)(ORN)(DLY)RW(ORN)(DAB)AK(DPR)P


Type: Cyclic peptide / Class: Antibiotic / Mass: 1713.079 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: Beta-Hairpin Peptidomimetic antibiotic TWL(DAB)(ORN)(DLY)RW(ORN)(DAB)AK(DPR)P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
1722D 1H-13C HSQC
1822D 1H-13C HMBC

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM protein, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
25 mM protein, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
5 mMentity-11
90 %H2O-21
10 %D2O-31
5 mMentity-42
100 %D2O-52
Sample conditionsIonic strength: 0 / pH: 2.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospinprocessing
XEASY1.53Bartels et al.chemical shift assignment
DYANA1.5Guntert, Braun and Wuthrichstructure solution
DYANAGuntert, Braun and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 181 / NOE intraresidue total count: 49 / NOE medium range total count: 48 / NOE sequential total count: 44
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.25 Å

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