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- PDB-2lte: Solution NMR structure of the specialized acyl carrier protein PA... -

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Basic information

Entry
Database: PDB / ID: 2lte
TitleSolution NMR structure of the specialized acyl carrier protein PA3334 (apo) from Pseudomonas aeruginosa, Northeast Structural Genomics Consortium Target PaT415
ComponentsSpecialized acyl carrier protein
KeywordsTRANSFERASE / acyl carrier protein / apo protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing, refinement in explicit water
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Cort, J.R. / Yang, Y. / Garcia, M. / Yee, A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the specialized acyl carrier protein PA3334 (apo) from Pseudomonas aeruginosa. Northeast Structural Genomics Consortium Target PaT415.
Authors: Ramelot, T.A. / Cort, J.R. / Yang, Y. / Garcia, M. / Yee, A. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionMay 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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:
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Assembly

Deposited unit
A: Specialized acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)11,5741
Polymers11,5741
Non-polymers00
Water00
1


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

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Components

#1: Protein Specialized acyl carrier protein


Mass: 11573.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: 2192 / Gene: PA2G_02747 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIPL / References: UniProt: A3LDD1

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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
1313D NUS 1H-15N NOESY
1413D NUS 1H-13C NOESY aliphatic
1513D 1H-13C NOESY aromatic
1624D 1H-13C-13C-1H NOESY
1713D HN(CA)CB
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HNCO
11113D (H)CCH-TOCSY
11213D C(CO)NH
11323D (H)CCH-TOCSY
11432D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] protein, 10 mM TRIS, 450 mM sodium chloride, 10 mM DTT, 0.01 mM zinc chloride, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-100% 13C; U-100% 15N] protein, 10 mM TRIS, 450 mM sodium chloride, 10 mM DTT, 0.01 mM zinc chloride, 0.01 % sodium azide, 100% D2O100% D2O
30.3 mM [U-100% 15N] 7% 13C from 13C glucose protein, 10 mM TRIS, 450 mM sodium chloride, 10 mM DTT, 0.01 mM zinc chloride, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-21
450 mMsodium chloride-31
10 mMDTT-41
0.01 mMzinc chloride-51
0.01 %sodium azide-61
1.0 mMprotein-7[U-100% 13C; U-100% 15N]2
10 mMTRIS-82
450 mMsodium chloride-92
10 mMDTT-102
0.01 mMzinc chloride-112
0.01 %sodium azide-122
0.3 mMprotein-13[U-100% 15N] 7% 13C from 13C glucose3
10 mMTRIS-143
450 mMsodium chloride-153
10 mMDTT-163
0.01 mMzinc chloride-173
0.01 %sodium azide-183
Sample conditionsIonic strength: 250 / pH: 7.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAVANCE III8501
Bruker AvanceIIIBrukerAVANCE III6002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004
Varian INOVAVarianINOVA5005

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
FMCGUI2.5 linux(FMCGUI) Alex Lemakrefinement
Sparky3.113Goddardpeak picking
TALOS+Version 1.2009.0721.18Shen, Cornilescu, Delaglio and Baxpredict dihedral angles
MDDGUIJune2009Alex Lemak, University of Torontoprocessing
NMRPipeNMRPipe-2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, refinement in explicit water / Software ordinal: 1
Details: CYANA-3.0 USED TO ASSIGN NOES AND TO CACULATE STRUCTURES AFTER MANUAL NOE EDITING CALC 100, KEEP 20, STEPS=15000, CNS_SOLVE_1.3 VIA FMCGUI, FMCGUI USED TO CONVERT FROM CYANA TO CNS, AND TO ...Details: CYANA-3.0 USED TO ASSIGN NOES AND TO CACULATE STRUCTURES AFTER MANUAL NOE EDITING CALC 100, KEEP 20, STEPS=15000, CNS_SOLVE_1.3 VIA FMCGUI, FMCGUI USED TO CONVERT FROM CYANA TO CNS, AND TO SET UP REFINEMENT PARAMETERS FOR CNS.
NMR constraintsNOE constraints total: 877
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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