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- PDB-2kgd: NMR Solution Structures of 3-oxo-butyl-ACP, an intermediate mimic... -

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Basic information

Entry
Database: PDB / ID: 2kgd
TitleNMR Solution Structures of 3-oxo-butyl-ACP, an intermediate mimic from the actinorhodin polyketide synthase in Streptomyces coelicolor
ComponentsActinorhodin polyketide synthase acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / ACP / polyketide mimic / diketide / Actinorhodin / Coelicolor / Antibiotic biosynthesis / Phosphopantetheine
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / antibiotic biosynthetic process / membrane / cytosol
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SXV / Actinorhodin polyketide synthase acyl carrier protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCrump, M.P. / Evans, S.E. / Williams, C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Probing the Interactions of Early Polyketide Intermediates with the Actinorhodin ACP from S. coelicolor A3(2).
Authors: Evans, S.E. / Williams, C. / Arthur, C.J. / Ploskon, E. / Wattana-Amorn, P. / Cox, R.J. / Crosby, J. / Willis, C.L. / Simpson, T.J. / Crump, M.P.
History
DepositionMar 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actinorhodin polyketide synthase acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6682
Polymers9,2391
Non-polymers4281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Actinorhodin polyketide synthase acyl carrier protein / ACP / actI ORF3


Mass: 9239.177 Da / Num. of mol.: 1 / Mutation: C17S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO5089, SCBAC28G1.15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q02054
#2: Chemical ChemComp-SXV / N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(3-oxobutyl)sulfanyl]ethyl}-beta-alaninamide


Mass: 428.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29N2O8PS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11012D 13C,15N Filtered TOCSY
11112D 13C,15N filtered NOESY
11212D 13C F2 filtered NOESY

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Sample preparation

DetailsContents: 1-2 mM 4 -phosphopantetheine chain derivatised with a 3-oxo-butyl group-1, 20 mM potassium phosphate-2, 1 mM sodium azide-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mM4 -phosphopantetheine chain derivatised with a 3-oxo-butyl group-11-21
20 mMpotassium phosphate-21
1 mMsodium azide-31
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Analysis_(CCPN)1Rasmus H. Fogh, Wim F. Vranken, Wayne Boucher, Tim J. Stevens and Ernest D. Lauechemical shift assignment
Analysis_(CCPN)1Rasmus H. Fogh, Wim F. Vranken, Wayne Boucher, Tim J. Stevens and Ernest D. Lauepeak picking
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES (SORTED ACCORDING TO TOTAL ...Details: ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES (SORTED ACCORDING TO TOTAL ENERGY) WERE SELECTED FOR WATER REFINEMENT. WATER REFINED STRUCTURES WERE CALCULATED USING THE SLIGHTLY MODIFIED REFINEMENT SCRIPT APPLIED TO THE RECOORD DATABASE. PROCHECK AND WHATCHECK AND QUALITY INDICATORS WERE COMPARED TO THE AVERAGE VALUES FOR THE RECOORD DATABASE OF PROTEIN NMR STRUCTURES.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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