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- PDB-2kor: NMR solution structures of 2-octenoyl-ACP from Streptomyces coeli... -

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Basic information

Entry
Database: PDB / ID: 2kor
TitleNMR solution structures of 2-octenoyl-ACP from Streptomyces coelicolor Fatty Acid Synthase
ComponentsAcyl carrier protein
KeywordsTRANSPORT PROTEIN / acyl carrier protein / intermediate binding / fatty acid synthase / Fatty acid biosynthesis / Lipid synthesis / Phosphopantetheine
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol
Similarity search - Function
EAL domain / EAL domain profile. / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SOO / Acyl carrier protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsPloskon, E. / Arthur, C.J. / Crump, M.P.
CitationJournal: Chem.Biol. / Year: 2010
Title: Recognition of intermediate functionality by acyl carrier protein over a complete cycle of fatty acid biosynthesis
Authors: Ploskon, E. / Arthur, C.J. / Kanari, A.L. / Wattana-amorn, P. / Williams, C. / Crosby, J. / Simpson, T.J. / Willis, C.L. / Crump, M.P.
History
DepositionSep 29, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2762
Polymers8,7941
Non-polymers4831
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 Acyl carrier protein


Mass: 8793.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: acpP, SCO2389, SC4A7.17 / Plasmid: Sc-apoFAS-pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P72393
#2: Chemical ChemComp-SOO / S-[2-[3-[[(2S)-2-hydroxy-3,3-dimethyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (E)-oct-2-enethioate


Mass: 482.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N2O8PS

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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 HN(CA)CB
1413D (H)CCH-TOCSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1712D 13C,15N Filtered NOESY
1812D 13C,15N Filtered TOCSY
1912D F2 13C Filtered NOESY

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Sample preparation

DetailsContents: 50mM potassium phosphate-1, 0.5mM sodium azide-2, 1mM 2-octenoyl phosphopantetheine-3, 1mM [U-99% 13C; U-99% 15N] ACP-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphate-11
0.5 mMsodium azide-21
1 mM2-octenoyl phosphopantetheine-31
1 mMACP-4[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue,Nilgesrefinement
ARIA1.2Linge, O'Donoghue, Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPN_Analysis1Fogh, Vranken, Boucher, Stevens, Lauedata analysis
CCPN_Analysis1Fogh, Vranken, Boucher, Stevens, Lauepeak picking
CCPN_Analysis1Fogh, Vranken, Boucher, Stevens, Lauechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 20 best structures from last iteration were selected for water refinement. Water refined structures were calculated using the slightly modified refinement script applied to the RECOORD database.
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 / Representative conformer: 1

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