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- PDB-5hvc: Solution structure of the apo state of the acyl carrier protein f... -

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Basic information

Entry
Database: PDB / ID: 5hvc
TitleSolution structure of the apo state of the acyl carrier protein from the MLSA2 subunit of the mycolactone polyketide synthase
ComponentsType I modular polyketide synthase
KeywordsTRANSFERASE / acyl carrier protein mycolactone
Function / homology
Function and homology information


phenol-containing compound biosynthetic process / toxin biosynthetic process / polyketide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
: / Polyketide synthase, docking domain superfmaily / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / ACP-like / Polyketide synthase, dehydratase domain ...: / Polyketide synthase, docking domain superfmaily / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, thioesterase domain / Thioesterase / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / ACP-like / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Alpha/Beta hydrolase fold / 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
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 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 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 / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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


Theoretical massNumber of molelcules
Total (without water)10,2371
Polymers10,2371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5390 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Type I modular polyketide synthase


Mass: 10237.473 Da / Num. of mol.: 1
Fragment: Acyl carrier protein fragment, UNP residues 2050 to 2140
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

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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-TOCSY-HSQC
131isotropic13D 15N-NOESY-HSQC
141isotropic13D HNCA
151isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA
171isotropic13D CBCA(CO)NH
161isotropic13D (H)CCH-TOCSY
191isotropic23D 13C-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 150 mM sodium phosphate, 0.1 mM 333-trimethylsilylpropionate, sodium salt, 90% H2O/10% D2O
Details: The sample was prepared at a concentration of 800 micromolar in phosphate buffer supplemented with 10 % D2O (Sigma) and 0.0025 % 3,3,3-trimethylsilylpropionate (Sigma) in 5 mm Ultra-Imperial ...Details: The sample was prepared at a concentration of 800 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 microlitres.
Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium phosphatenatural abundance1
0.1 mM333-trimethylsilylpropionate, sodium saltnatural abundance1
Sample conditionsIonic strength: 150 mM / Ionic strength err: 25 / Label: conditions_1 / pH: 7.5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 283 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
Details: The structures are based on 2839 distance restraints, no hydrogen bond restraints, and 167 backbone dihedral angle restraints defined using the DANGLE algorithm in CCPN Analysis
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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