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- PDB-6h0j: A1-type ACP domain from module 5 of MLSA1 -

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Basic information

Entry
Database: PDB / ID: 6h0j
TitleA1-type ACP domain from module 5 of MLSA1
ComponentsType I modular polyketide synthase
KeywordsPROTEIN BINDING / ACYL CARRIER PROTEIN MYCOLACTONE POLYKETIDE SYNTHASE
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / ACP-like / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / ACP-like / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Type I modular polyketide synthase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMoretto, L. / Heylen, R. / Holroyd, N. / Vance, S. / Broadhurst, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust094252/Z/10/Z United Kingdom
CitationJournal: Sci Rep / Year: 2019
Title: Modular type I polyketide synthase acyl carrier protein domains share a common N-terminally extended fold.
Authors: Moretto, L. / Heylen, R. / Holroyd, N. / Vance, S. / Broadhurst, R.W.
History
DepositionJul 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type I modular polyketide synthase


Theoretical massNumber of molelcules
Total (without water)10,6081
Polymers10,6081
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 area5070 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Type I modular polyketide synthase


Mass: 10607.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A fragment from the fifth chain extension module of the MLSA1 subunit of the mycolactone polyketide synthase system
Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria)
Strain: Agy99 / Gene: mlsA1, MUP040c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q6MZA4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
123isotropic33D 1H-15N NOESY
242isotropic13D HNCA
252isotropic13D HN(CO)CA
272isotropic13D HN(CA)CB
262isotropic13D CBCA(CO)NH
282isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution20.8 mM [U-13C; U-15N] mH0ACPa, 150 mM sodium chloride, 45 mM sodium phosphate, 90% H2O/10% D2O800 micromolar in phosphate buffer supplemented with 10 % D2O (Sigma) and 0.0025 % 3,3,3-trimethylsilylpropionate (Sigma) in 5 mm Ultra-Imperial grade NMR tubes (Wilmad) to a final volume of 600 microlitres13C15N_mH0ACPa90% H2O/10% D2O
solution30.8 mM [U-15N] mH0ACPa, 150 mM sodium chloride, 45 mM sodium phosphate, 90% H2O/10% D2O800 micromolar in phosphate buffer supplemented with 10 % D2O (Sigma) and 0.0025 % 3,3,3-trimethylsilylpropionate (Sigma) in 5 mm Ultra-Imperial grade NMR tubes (Wilmad) to a final volume of 600 microlitres15N_mH0ACPa90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMmH0ACPa[U-13C; U-15N]2
150 mMsodium chloridenatural abundance2
45 mMsodium phosphatenatural abundance2
0.8 mMmH0ACPa[U-15N]3
150 mMsodium chloridenatural abundance3
45 mMsodium phosphatenatural abundance3
Sample conditions

Ionic strength: 150 mM / Ionic strength err: 10 / pH: 7.5 pD / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.5

Conditions-IDLabel
115N_mH0ACPa
213C15N_mH0ACPa

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AzaraBoucherprocessing
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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