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- PDB-2mbz: Structural Basis of a Thiopeptide Antibiotic Multidrug Resistance... -

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Basic information

Entry
Database: PDB / ID: 2mbz
TitleStructural Basis of a Thiopeptide Antibiotic Multidrug Resistance System from Streptomyces lividans:Promothiocin A in Complex with TipAS
Components
  • HTH-type transcriptional activator TipA
  • Promothiocin A
KeywordsTRANSCRIPTION ACTIVATOR/ANTIBIOTIC / TipAS/Promothiocin A / protein/antibiotic / protein/thiopeptide / multidrug recognition / transcriptional activator / TRANSCRIPTION ACTIVATOR-ANTIBIOTIC complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Promothiocin A / HTH-type transcriptional activator TipA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHabazettl, J. / Allan, M.G. / Jensen, P. / Sass, H. / Grzesiek, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Structural basis and dynamics of multidrug recognition in a minimal bacterial multidrug resistance system.
Authors: Habazettl, J. / Allan, M. / Jensen, P.R. / Sass, H.J. / Thompson, C.J. / Grzesiek, S.
History
DepositionAug 12, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_entity_src_syn
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.src_method
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / 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 / _pdbx_nmr_software.name / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional activator TipA
B: Promothiocin A


Theoretical massNumber of molelcules
Total (without water)17,5262
Polymers17,5262
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HTH-type transcriptional activator TipA


Mass: 16584.104 Da / Num. of mol.: 1 / Fragment: UNP residues 110-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: tipA / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P0A4T9
#2: Protein/peptide Promothiocin A


Type: Thiopeptide / Class: Antibiotic / Mass: 942.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Promothiocin A

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
3232D 1H-13C HSQC aliphatic
2323D HNCO
2423D CBCA(CO)NH
2523D C(CO)NH TOCSY
2623D HBHA(CO)NH
2723D H(CCO)NH TOCSY
3833D (H)CCH-TOCSY aliphatic
2923D HNHA
3103HAHB
2112CBCANH
212213C'-{13C } spin-echo difference 1H-15N HSQC
213215N-{13C } spin-echo difference 1H-15N HSQC
214213C'-{13C } spin-echo difference 1H-13C HSQC
215215N-{13C } spin-echo difference 1H-13C HSQC
11613D 1H-15N ROESY
11713D 1H-15N NOESY
31833D 1H-13C NOESY
31934D 13C-13C-NOESY-HMQC
32032D NOESY filtered against 1H bound to 13C or 15N
22122D NOESY filtered against 1H bound to 13C or 15N
32232D HOHAHA filtered against 1H bound to 13C or 15N
2232Doublet-separated sensitivity-enhanced 1H-15N HSQC
4244Doublet-separated sensitivity-enhanced 1H-15N HSQC
2252J-resolved constant-time 13C-HSQC
4264J-resolved constant-time 13C-HSQC
32733D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 15N] TipAS-1, 2 mM promothiocin A-2, 50 mM potassium phosphate-3, 0.02 w/v sodium azide-4, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12, 100% D2O100% D2O
40.8 mM [U-100% 13C; U-100% 15N] TipAS-13, 1.6 mM promothiocin A-14, 10 mM potassium phosphate-15, 10 mg/mL Pf1 phage-16, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTipAS-1[U-98% 15N]1
2 mMpromothiocin A-21
50 mMpotassium phosphate-31
0.02 w/vsodium azide-41
1 mMTipAS-5[U-100% 13C; U-100% 15N]2
2 mMpromothiocin A-62
50 mMpotassium phosphate-72
0.02 w/vsodium azide-82
1 mMTipAS-9[U-100% 13C; U-100% 15N]3
2 mMpromothiocin A-103
50 mMpotassium phosphate-113
0.02 w/vsodium azide-123
0.8 mMTipAS-13[U-100% 13C; U-100% 15N]4
1.6 mMpromothiocin A-144
10 mMpotassium phosphate-154
10 mg/mLPf1 phage-164
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.0555.9ambient 298 K
20.0555.9ambient 298 K
30.0555.9ambient 298 K
40.0555.9ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipe2012Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.115Goddardpeak picking
Sparky3.115Goddardchemical shift assignment
PIPPGarrettpeak picking
XEASYBartels et al.chemical shift assignment
TALOStalos+Cornilescu, Delaglio and Baxdihedral angle prediction
ProcheckNMRLaskowski and MacArthurstructure analysis
XwinNMRBruker Biospinexperiment/data collection
TopSpinBruker Biospinexperiment/data collection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1st. simulated annealing step: ligand is covalently attached, but only restraints of the folded part of the protein in apo form are used 2nd. simulated annealing step: all restraints are used
NMR constraintsNOE constraints total: 1704 / NOE intraresidue total count: 75 / NOE long range total count: 423 / NOE medium range total count: 607 / NOE sequential total count: 555 / Hydrogen bond constraints total count: 120 / Protein chi angle constraints total count: 22 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 128 / Protein psi angle constraints total count: 128
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 4.9 ° / Maximum upper distance constraint violation: 0.49 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.038 Å / Distance rms dev error: 0.002 Å

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