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- PDB-5hv8: Solution structure of an octanoyl- loaded acyl carrier protein do... -

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Basic information

Entry
Database: PDB / ID: 5hv8
TitleSolution structure of an octanoyl- loaded acyl carrier protein domain from module MLSA2 of the mycolactone polyketide synthase.
ComponentsType I modular polyketide synthase
KeywordsTRANSFERASE / acyl carrier protein mycolactone
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Zinc-binding dehydrogenase / Polyketide synthase, thioesterase domain / Thioesterase / ACP-like / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Polyketide synthase, docking domain superfmaily / Zinc-binding dehydrogenase / Polyketide synthase, thioesterase domain / Thioesterase / ACP-like / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-66S / Type I modular polyketide synthase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsVance, S. / Tkachenko, O. / Thomas, B. / Bassuni, M. / Hong, H. / Nietlispach, D. / Broadhurst, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust094252/Z/10/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2016
Title: Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase.
Authors: Vance, S. / Tkachenko, O. / Thomas, B. / Bassuni, M. / Hong, H. / Nietlispach, D. / Broadhurst, W.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.5Oct 23, 2019Group: Data collection / Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions / Item: _pdbx_nmr_exptl_sample_conditions.temperature_units

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type I modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7222
Polymers10,2371
Non-polymers4851
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5780 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: 10237.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Gene: mlsA2, MUP039c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner / References: UniProt: Q6MZA5
#2: Chemical ChemComp-66S / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] octanethioate


Mass: 484.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H37N2O8PS / Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Gene: mlsA2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3)

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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
121isotropic13D 15N-HSQC-TOCSY
131isotropic13D 15N-HSQC-NOESY
141isotropic13D HNCA
151isotropic13D HN(CO)CA
1131isotropic13D HN(CA)CB
1121isotropic13D CBCA(CO)NH
1111isotropic13D (H)CCH-TOCSY
1101isotropic23D 13C-HSQC-NOESY

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Sample preparation

DetailsType: solution
Contents: 150 mM sodium phosphate, 0.1 mM 3,3,3-trimethylsilylpropionate, sodium salt, 90% H2O/10% D2O
Details: The sample was prepared at a concentrations of 800 micromolar in phosphate buffer supplemented with 10 % D2O and 0.0025 % 3,3,3-trimethylsilylpropionate (Sigma) in 5 mm Ultra-Imperial grade ...Details: The sample was prepared at a concentrations of 800 micromolar in phosphate buffer supplemented with 10 % D2O and 0.0025 % 3,3,3-trimethylsilylpropionate (Sigma) in 5 mm Ultra-Imperial grade NMR tubes (Wilmad) to a final volume of 600 microlitres.
Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium phosphatenatural abundance1
0.1 mM3,3,3-trimethylsilylpropionate, sodium saltnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 283 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
Details: Structures were calculated with no hydrogen bond restraints, and 167 dihedral angle restraints determined using DANGLE
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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