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- PDB-2lpk: Solution NMR of the specialized apo-acyl carrier protein (RPA2022... -

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Basic information

Entry
Database: PDB / ID: 2lpk
TitleSolution NMR of the specialized apo-acyl carrier protein (RPA2022) from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR324
ComponentsSpecialized acyl carrier protein
KeywordsTRANSFERASE / apo / PSI-Biology / AcpXL / RpAcpXL / Structural Genomics / Northeast Structural Genomics Consortium / Protein Structure Initiative / NESG
Function / homology
Function and homology information


fatty acid biosynthetic process
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 AcpXL
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Rossi, P. / Yang, Y. / Lee, H. / Ertekin, A. / Wang, H. / Ciccosanti, C. / Kohan, E. / Maglaqui, M. / Janjua, H. ...Ramelot, T.A. / Rossi, P. / Yang, Y. / Lee, H. / Ertekin, A. / Wang, H. / Ciccosanti, C. / Kohan, E. / Maglaqui, M. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Biochemistry / Year: 2012
Title: Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long-chain fatty acids in open and closed conformations.
Authors: Ramelot, T.A. / Rossi, P. / Forouhar, F. / Lee, H.W. / Yang, Y. / Ni, S. / Unser, S. / Lew, S. / Seetharaman, J. / Xiao, R. / Acton, T.B. / Everett, J.K. / Prestegard, J.H. / Hunt, J.F. / ...Authors: Ramelot, T.A. / Rossi, P. / Forouhar, F. / Lee, H.W. / Yang, Y. / Ni, S. / Unser, S. / Lew, S. / Seetharaman, J. / Xiao, R. / Acton, T.B. / Everett, J.K. / Prestegard, J.H. / Hunt, J.F. / Montelione, G.T. / Kennedy, M.A.
History
DepositionFeb 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Specialized acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)11,3101
Polymers11,3101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Specialized acyl carrier protein


Mass: 11309.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA2022 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q6N882

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1422D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliph
1713D 1H-13C NOESY arom
1812D 1H-15N hetNOE
1912D 1H-15N T1
11012D 1H-15N T2
11111D 15N T1
11211D 15N T2

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 5 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 5 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
10 mMDTT-61
5 uMDSS-71
1.0 mMprotein-8[U-100% 13C; U-100% 15N]2
20 mMMES-92
200 mMsodium chloride-102
5 mMcalcium chloride-112
0.02 %sodium azide-122
10 mMDTT-132
5 uMDSS-142
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502
Bruker AvanceIIIBrukerAVANCE III6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
PdbStat5.4(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
CYANA__3.03Guntert, Mumenthaler and Wuthrichstructure solution
FMCGUIAlex Lemak, University of Torontorefinement
PALESpales_linuxZweckstetterrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement + RDCs
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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