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- PDB-2mc0: Structural Basis of a Thiopeptide Antibiotic Multidrug Resistance... -

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Basic information

Entry
Database: PDB / ID: 2mc0
TitleStructural Basis of a Thiopeptide Antibiotic Multidrug Resistance System from Streptomyces lividans:Nosiheptide in Complex with TipAS
Components
  • HTH-type transcriptional activator TipA
  • nosiheptide
KeywordsTRANSCRIPTION ACTIVATOR/ANTIBIOTIC / bacterial protein / Streptomyces lividans / transcriptional activation / TipAS-nosiheptide complex / transcriptional activator-antibiotic complex / protein/thiopeptide / multidrug recognition / 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 / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
nosiheptide bound form / Chem-NO1 / HTH-type transcriptional activator TipA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Streptomyces actuosus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHabazettl, J. / Allan, M.G. / Jensen, P. / Sass, H. / Grzesiek, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / 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 1.1Dec 9, 2015Group: Database references
Revision 2.0Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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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: nosiheptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9873
Polymers17,7812
Non-polymers2051
Water0
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 nosiheptide /


Type: Thiopeptide / Class: Antibiotic / Mass: 1197.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces actuosus (bacteria) / References: nosiheptide bound form
#3: Chemical ChemComp-NO1 / 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid


Type: Thiopeptide / Class: Antibiotic / Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3 / References: nosiheptide bound form

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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
2623D HBHA(CO)NH
2723D HC(CO)NH TOCSY
3833D (H)CCH-TOCSY
1913D HNHA
11013D 1H-15N NOESY
31133D 1H-13C NOESY aliphatic
31233D 1H-13C NOESY aromatic
31332D 1H-1H NOESY/filter against 13C-15N
21422D 1H-1H NOESY/filter against 13C-15N
31532D 1H-1H TOCSY/filter against 13C-15N
2162Doublet-separated 2D 1H-15N HSQC
4174Doublet-separated 2D 1H-15N HSQC
2182J-resolved ct 13C-HSQC
4194J-resolved ct 13C-HSQC
22023D CBCANH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 15N] TipAS-1, 2 mM nosiheptide-2, 50 mM potassium phosphate-3, 0.02 w/v sodium azide-4, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-99% 13C; U-99% 15N] TipAS-5, 2 mM nosiheptide-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-99% 13C; U-99% 15N] TipAS-9, 2 mM nosiheptide-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12, 100% D2O100% D2O
40.8 mM [U-99% 13C; U-99% 15N] TipAS-13, 1.6 mM nosiheptide-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 mMnosiheptide-21
50 mMpotassium phosphate-31
0.02 w/vsodium azide-41
1 mMTipAS-5[U-99% 13C; U-99% 15N]2
2 mMnosiheptide-62
50 mMpotassium phosphate-72
0.02 w/vsodium azide-82
1 mMTipAS-9[U-99% 13C; U-99% 15N]3
2 mMnosiheptide-103
50 mMpotassium phosphate-113
0.02 w/vsodium azide-123
0.8 mMTipAS-13[U-99% 13C; U-99% 15N]4
1.6 mMnosiheptide-144
10 mMpotassium phosphate-154
10 mg/mLPf1 phage-164
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.055 5.9 ambient 298 K
20.055 5.9 ambient 298 K
30.055 ambient 298 K
40.011 5.9 ambient 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
Xplor-NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
Xplor-NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipe2012Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.115Goddardchemical shift assignment
Sparky3.115Goddardpeak picking
TopSpinBruker Biospinexperiment/data collection
PIPPGarrettpeak picking
XEASYBartels et al.chemical shift assignment
TALOSTALOS+Cornilescu, Delaglio and Baxdihedral angle prediction
ProcheckNMRLaskowski and MacArthurstructure analysis
XwinNMRBruker 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: 2265 / NOE intraresidue total count: 253 / NOE long range total count: 599 / NOE medium range total count: 771 / NOE sequential total count: 648 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 130 / Protein psi angle constraints total count: 130
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 lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.038 Å / Distance rms dev error: 0.002 Å

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