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- PDB-8all: NMR structure of holo-acp -

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Basic information

Entry
Database: PDB / ID: 8all
TitleNMR structure of holo-acp
ComponentsHybrid non ribosomal peptide synthetase-polyketide synthase
KeywordsTRANSFERASE / Acyl carrier protein
Function / homology
Function and homology information


polyketide biosynthetic process / : / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / 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, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / 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 / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Hybrid non ribosomal peptide synthetase-polyketide synthase
Similarity search - Component
Biological speciesStreptomyces virginiae (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCollin, S. / Weissman, K.J. / Chagot, B. / Gruez, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Commun / Year: 2023
Title: Decrypting the programming of beta-methylation in virginiamycin M biosynthesis.
Authors: Collin, S. / Cox, R.J. / Paris, C. / Jacob, C. / Chagot, B. / Weissman, K.J. / Gruez, A.
History
DepositionAug 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hybrid non ribosomal peptide synthetase-polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2962
Polymers8,9381
Non-polymers3581
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area290 Å2
ΔGint-4 kcal/mol
Surface area5890 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Hybrid non ribosomal peptide synthetase-polyketide synthase


Mass: 8938.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces virginiae (bacteria) / Gene: virG / Production host: Escherichia coli (E. coli) / References: UniProt: A4PHM4
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HNCA
1111isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY
191isotropic13D 1H-13C NOESY aromatic
181isotropic13D (H)CCH-TOCSY
171isotropic13D CCH-TOCSY
161isotropic13D HNHA
1151isotropic12D 1H(C12 N14) -1H(C12 N14) TOCSY
1141isotropic12D 1H-1H(C12 N14) NOESY
1131isotropic12D 1H(C12 N14)-1H(C12 N14) NOESY

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Sample preparation

DetailsType: solution
Contents: 1.6 mM [U-100% 13C; U-100% 15N] Hybrid polyketide synthase-non ribosomal peptide synthetase ACP7, 100 mM sodium phosphate, 1 mM TCEP, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMHybrid polyketide synthase-non ribosomal peptide synthetase ACP7[U-100% 13C; U-100% 15N]1
100 mMsodium phosphatenatural abundance1
1 mMTCEPnatural abundance1
Sample conditionsIonic strength: 0.1 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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