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- PDB-2mai: NMR structure of lassomycin -

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Basic information

Entry
Database: PDB / ID: 2mai
TitleNMR structure of lassomycin
ComponentsLassomycin
KeywordsANTIBIOTIC / lasso
Biological speciesLentzea kentuckyensis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsGavrish, E. / Sit, C.S. / Kandror, O. / Spoering, A. / Peoples, A. / Ling, L. / Fetterman, A. / Hughes, D. / Cao, S. / Bissell, A. ...Gavrish, E. / Sit, C.S. / Kandror, O. / Spoering, A. / Peoples, A. / Ling, L. / Fetterman, A. / Hughes, D. / Cao, S. / Bissell, A. / Torrey, H. / Akopian, T. / Mueller, A. / Epstein, S. / Goldberg, A. / Clardy, J. / Lewis, K.
CitationJournal: Chem.Biol. / Year: 2014
Title: Lassomycin, a Ribosomally Synthesized Cyclic Peptide, Kills Mycobacterium tuberculosis by Targeting the ATP-Dependent Protease ClpC1P1P2.
Authors: Gavrish, E. / Sit, C.S. / Cao, S. / Kandror, O. / Spoering, A. / Peoples, A. / Ling, L. / Fetterman, A. / Hughes, D. / Bissell, A. / Torrey, H. / Akopian, T. / Mueller, A. / Epstein, S. / ...Authors: Gavrish, E. / Sit, C.S. / Cao, S. / Kandror, O. / Spoering, A. / Peoples, A. / Ling, L. / Fetterman, A. / Hughes, D. / Bissell, A. / Torrey, H. / Akopian, T. / Mueller, A. / Epstein, S. / Goldberg, A. / Clardy, J. / Lewis, K.
History
DepositionJul 9, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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:
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Assembly

Deposited unit
A: Lassomycin


Theoretical massNumber of molelcules
Total (without water)1,9011
Polymers1,9011
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Lassomycin


Mass: 1901.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lentzea kentuckyensis (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D HNHA
1713D 1H-15N TOCSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 4 mM [U-100% 13C; U-100% 15N] protein, DMSO / Solvent system: DMSO
SampleConc.: 4 mM / Component: entity_1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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