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- PDB-6lvt: Solution structure of holo acyl carrier protein from Thermotoga m... -

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Basic information

Entry
Database: PDB / ID: 6lvt
TitleSolution structure of holo acyl carrier protein from Thermotoga maritima
ComponentsAcyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / acyl carrier protein
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol
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 speciesThermotoga maritima MSB8 (bacteria)
MethodSOLUTION NMR / na
AuthorsLee, Y. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)S201903S00006 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Characterization of an ACP from Thermotoga maritima : Insights into Hyperthermal Adaptation.
Authors: Lee, Y. / Jang, A. / Jeong, M.C. / Park, N. / Park, J. / Lee, W.C. / Cheong, C. / Kim, Y.
History
DepositionFeb 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _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)8,9061
Polymers8,9061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4910 Å2
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: 8905.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: acpP / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZD0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC
133isotropic13D HN(CA)CB
143isotropic13D CBCA(CO)NH
153isotropic13D HNCO
163isotropic13D C(CO)NH
173isotropic13D HBHA(CO)NH
183isotropic13D H(CCO)NH
191isotropic12D 1H-1H TOCSY
1101isotropic12D 1H-1H NOESY
1113isotropic13D 1H-15N NOESY
1123isotropic13D 1H-13C NOESY aliphatic
1133isotropic13D 1H-13C NOESY aromatic
1142isotropic12D HSQC-DSSE(IPAP)
2152anisotropic12D HSQC-DSSE(IPAP)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM ACP, 90% H2O/10% D2Onon-labeled sample90% H2O/10% D2O
solution20.5 mM [U-99% 15N] ACP, 90% H2O/10% D2O15N sample90% H2O/10% D2O
solution30.5 mM [U-99% 13C; U-99% 15N] ACP, 90% H2O/10% D2O13C/15N sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMACPnatural abundance1
0.5 mMACP[U-99% 15N]2
0.5 mMACP[U-99% 13C; U-99% 15N]3
Sample conditions
Conditions-IDDetailsIonic strength unitsLabelpHPressure (kPa)Temperature (K)
125mM MES, 5mM CaCl2, 5mM DTT, 50nM DSS, 0.5mg/mL NaN3Not definedbuffer6.1 1 atm298 K
25% acrylamide, 25mM MES, 5mM CaCl2, 5mM DTT, 50nM DSS, 0.5mg/mL NaN3Not definedpolyacrylamide gel6.1 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee, Tonelli and Markleypeak picking
NMRFAM-SPARKYLee, Tonelli and Markleychemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Cornilescu, Dashti, Eghbalnia, Tonelli, Westler, Butcher, Wildman-Henzler and Markleyrefinement
RefinementMethod: na / Software ordinal: 6
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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