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- PDB-9l1v: Solution structure of holo Acyl carrier protein 2 (ApeF) of aryl ... -

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Basic information

Entry
Database: PDB / ID: 9l1v
TitleSolution structure of holo Acyl carrier protein 2 (ApeF) of aryl polyene biosynthesis from Acinetobacter baumannii
ComponentsAcyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / PROTEIN TRANSPORT
Function / homologyacyl carrier activity / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / cytoplasm / Acyl carrier protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodSOLUTION NMR / na
AuthorsLee, C. / Yoo, S. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00207959 Korea, Republic Of
CitationJournal: Protein Sci. / Year: 2025
Title: Structural and dynamic roles of tandem acyl carrier proteins in aryl polyene biosynthesis in carbapenem-resistant Acinetobacter baumannii.
Authors: Lee, C.Y. / Son, M. / Lee, W.C. / Yoo, S. / Choi, S. / Kim, E. / Hwang, E. / Kim, Y.
History
DepositionDec 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed

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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)9,4481
Polymers9,4481
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


Mass: 9447.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: acpM, acpP, AUO97_09980, B9W25_05115, SAMEA4394745_03147
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059ZU64
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
111isotropic12D 1H-15N HSQC
123isotropic13D HNCO
133isotropic13D HN(CA)CB
143isotropic13D CBCA(CO)NH
153isotropic13D HBHA(CO)NH
163isotropic13D H(CCO)NH
173isotropic13D C(CO)NH
182isotropic12D 1H-1H NOESY
192isotropic12D 1H-1H TOCSY
1101isotropic13D 1H-15N NOESY
1113isotropic13D 1H-13C NOESY

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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 mM sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-100% 15N] Acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2OLB90% H2O/10% D2O
solution30.5 mM [U-100% 15N] Acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% 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 mMsodium azidenatural abundance1
0.5 mMAcyl carrier protein[U-100% 15N]2
25 mMMESnatural abundance2
5 mMcalcium chloridenatural abundance2
5 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
0.5 mMAcyl carrier protein[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, Tonelii and Markleychemical shift assignment
NMRFAM-SPARKYLee, Tonelii 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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