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- PDB-9wab: Solution structure of holo Acyl carrier protein from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9wab
TitleSolution structure of holo Acyl carrier protein from Escherichia coli
ComponentsAcyl carrier protein
KeywordsPROTEIN TRANSPORT / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / membrane / cytosol / cytoplasm
Similarity search - Function
Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / na
AuthorsJang, S. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2025
Title: Structural and Dynamic Insights into Acyl Carrier Protein upon Metal Binding and Acylation Revealed by NMR Spectroscopy and MD Simulations.
Authors: Lee, C.Y. / Jang, S. / Cho, H. / Jeong, M.C. / Oh, Y. / Kim, Y.
History
DepositionAug 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)8,5141
Polymers8,5141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8514.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: acpP, b1094, JW1080 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6A8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
123isotropic23D HNCO
133isotropic23D HN(CA)CB
143isotropic23D CBCA(CO)NH
153isotropic23D HBHA(CO)NH
163isotropic23D H(CCO)NH
173isotropic23D C(CO)NH
182isotropic22D 1H-1H NOESY
191isotropic23D 1H-15N NOESY
1103isotropic23D 1H-13C NOESY
1113isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-100% 15N] Acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM Acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2OLB90% H2O/10% D2O
solution30.5 mM [U-100% 13C; U-100% 15N] Acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O13C, 15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAcyl carrier protein[U-100% 15N]1
25 mMMESnatural abundance1
5 mMcalcium chloridenatural abundance1
5 mMDTTnatural abundance1
0.02 %sodium azidenatural abundance1
0.5 mMAcyl carrier proteinnatural abundance2
25 mMMESnatural abundance2
5 mMcalcium chloridenatural abundance2
5 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
0.5 mMAcyl carrier protein[U-100% 13C; U-100% 15N]3
25 mMMESnatural abundance3
5 mMcalcium chloridenatural abundance3
5 mMDTTnatural abundance3
0.02 %sodium azidenatural abundance3
Sample conditionsIonic strength: 5 mM / Label: conditions_1 / pH: 6.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCE III HDBrukerAVANCE III HD7002

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Processing

NMR software
NameDeveloperClassification
PONDEROSA-C/SLee, Stark and Markleyrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Stark and Markleychemical shift calculation
NMRFAM-SPARKYLee, Tonelli and Markleychemical shift assignment
NMRFAM-SPARKYLee, Tonelli and Markleypeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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