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- PDB-7e42: Solution strucutre of holo acyl carrier protein from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 7.0E+42
TitleSolution strucutre of holo acyl carrier protein from Acinetobacter baumannii
ComponentsAcyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / acyl carrier protein / acinetobacter baumannii
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodSOLUTION NMR / na
AuthorsChoi, S. / Park, J. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)S201903S00006 Korea, Republic Of
CitationJournal: To Be Published
Title: solution structure of holo acyl carrier protein in acinetobacter baumannii
Authors: Choi, S. / Park, J. / Kim, Y.
History
DepositionFeb 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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

Downloads & links

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Assembly

Deposited unit
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)8,6751
Polymers8,6751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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: 8674.571 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: acpP, acpP_1, A7M79_02500, A7M90_13800, A9843_07390, AA954_11690, AB552B1_00559, AB71191_02236, AB901B6_02682, AB945B12_01328, ABC003_01415, ABCAM1_0761, ABKPCSM17A_02555, ABUW_3107, B4R90_ ...Gene: acpP, acpP_1, A7M79_02500, A7M90_13800, A9843_07390, AA954_11690, AB552B1_00559, AB71191_02236, AB901B6_02682, AB945B12_01328, ABC003_01415, ABCAM1_0761, ABKPCSM17A_02555, ABUW_3107, B4R90_07745, B9W69_04050, B9X95_05715, BGC29_09160, C2U32_18370, CEJ64_13015, CHQ89_11435, CPI82_11020, CSB70_0490, DLI67_08260, DLI69_06490, DLI75_02485, DOL94_00650, DVA69_14465, E2533_13480, E2535_15960, E2540_16920, EA667_015135, EA685_07000, EA686_08845, EA706_03190, EA722_03690, EKS29_20230, EWO92_12310, EWO96_16395, EWP49_14855, F4T91_07160, F4U04_04845, F8B16_05690, FD887_09470, FD913_04770, FDO31_02470, FGL68_16335, FJU36_15150, FJU42_04970, FJU76_14985, FJU79_08995, FJU87_10855, FJV14_09525, FR761_05255, G3N45_07055, GNY86_00055, GSE42_04680, GUK62_09305, IX87_18425, LV38_02925, NCTC13305_01644, NCTC13420_02175, NT90_07370, SAMEA104305215_02050, SAMEA104305261_00624, SAMEA104305318_02348, SAMEA104305351_01935
Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: V5VGC7

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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
121isotropic13D HNCO
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HBHA(CO)NH
161isotropic13D H(CCO)NH
171isotropic13D C(CO)NH
182isotropic12D 1H-1H NOESY
193isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY
1113isotropic22D HSQC-DSSE(IPAP)
2123anisotropic22D HSQC-DSSE(IPAP)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 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
solution20.5 mM acyl carrier protein, 25 mM MES, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2Onon-labeled sample90% 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% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMacyl carrier protein[U-100% 13C; 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% 15N]3
25 mMMESnatural abundance3
5 mMcalcium chloridenatural abundance3
5 mMDTTnatural abundance3
0.02 %sodium azidenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
115 mM1_buffer6.11 atm298 K
215 mM2_polyacrylamide gel6.11 atm298 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 Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Stark and Markleystructure 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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