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- PDB-6tg5: Solution structure of MacpD, a acyl carrier protein, from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 6tg5
TitleSolution structure of MacpD, a acyl carrier protein, from Pseudomonas fluorescens involved in Mupirocin biosynthesis.
ComponentsMacpD
KeywordsBIOSYNTHETIC PROTEIN / Mupirocin / acyl carrier protein / Acyl Starter units / Thiomarinol / Biosynthesis / Pseudomonas fluorescens
Function / homologyPhosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / MacpD
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWilliams, C. / Crump, M.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R007853/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L01386X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L015366/1 United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: A Priming Cassette Generates Hydroxylated Acyl Starter Units in Mupirocin and Thiomarinol Biosynthesis.
Authors: Walker, P.D. / Rowe, M.T. / Winter, A.J. / Weir, A.N.M. / Akter, N. / Wang, L. / Race, P.R. / Williams, C. / Song, Z. / Simpson, T.J. / Willis, C.L. / Crump, M.P.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MacpD


Theoretical massNumber of molelcules
Total (without water)14,9371
Polymers14,9371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7790 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the least restraint violations
RepresentativeModel #1medoid

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Components

#1: Protein MacpD


Mass: 14936.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-33 are vector derived Cysteine 80 has been mutated to a alanine for structural studies
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: macpD / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RL52

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic12D 1H-1H NOESY
132isotropic13D HNCO
142isotropic13D HNCA
1152isotropic13D HN(CO)CA
152isotropic13D C(CO)NH
1102isotropic13D CBCA(CO)NH
192isotropic13D HN(CA)CB
182isotropic13D (H)CCH-TOCSY
172isotropic23D (H)CCH-TOCSY
162isotropic13D 1H-13C NOESY
1122isotropic23D 1H-13C NOESY
1111isotropic13D 1H-15N NOESY
1141isotropic13D 1H-15N TOCSY
1132isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 15N] MacpD, acyl carrier protein, 0.1 mM sodium azide, 50 mM sodium phosphate, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM [U-99% 13C; U-99% 15N] MacpD, acyl carrier protein, 50 mM sodium phosphate, 0.1 mM sodium azide, 90% H2O/10% D2O15N/13C sample90% H2O/10% D2O
solution31 mM MacpD, acyl carrier protein, 50 mM sodium phosphate, 90% H2O/10% D2Ounlabelled sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMacpD, acyl carrier protein[U-99% 15N]1
0.1 mMsodium azidenatural abundance1
50 mMsodium phosphatenatural abundance1
1 mMMacpD, acyl carrier protein[U-99% 13C; U-99% 15N]2
50 mMsodium phosphatenatural abundance2
0.1 mMsodium azidenatural abundance2
1 mMMacpD, acyl carrier proteinnatural abundance3
50 mMsodium phosphatenatural abundance3
Sample conditionsDetails: 50mM sodium phosphate / Ionic strength: 50 mM / Ionic strength err: 0.2 / Label: buffer / pH: 6.7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Agilent VNMRSAgilentVNMRS6001cryoprobe
Bruker AVANCE IIIBrukerAVANCE III70021.7mm micro-cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpin3.5Bruker Biospincollection
VNMR4variancollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 250 / Conformers submitted total number: 20

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