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- PDB-8gsa: Solution structure of holo acyl carrier protein A from Enterococc... -

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Basic information

Entry
Database: PDB / ID: 8gsa
TitleSolution structure of holo acyl carrier protein A from Enterococcus faecalis
ComponentsAcyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / acyl carrier protein / Enterococcus faecalsi
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 speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / na
AuthorsYeon, J. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural study of acyl carrier protein of Enterococcus faecalis and its interaction with enzymes in de novo fatty acid synthesis.
Authors: Yeon, J. / Oh, S. / Hwang, E. / Kim, E. / Kim, Y.
History
DepositionSep 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI

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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)8,6191
Polymers8,6191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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: 8619.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: acpP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1B4XRD4

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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
121isotropic23D HNCO
131isotropic23D HN(CA)CB
141isotropic23D CBCA(CO)NH
151isotropic23D HBHA(CO)NH
171isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
1101isotropic12D 1H-1H TOCSY
191isotropic13D 1H-13C NOESY
181isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solid
Contents: 0.5 mM [U-13C; U-15N] Acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O
Label: 15N 13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAcyl carrier protein[U-13C; U-15N]1
25 mMMESnatural abundance1
5 mMcalcium chloridenatural abundance1
5 mMDTTnatural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: 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
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Stark, and Markleyrefinement
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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