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- PDB-2mii: NMR structure of E. coli LpoB -

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Basic information

Entry
Database: PDB / ID: 2mii
TitleNMR structure of E. coli LpoB
ComponentsPenicillin-binding protein activator LpoB
KeywordsPROTEIN BINDING / LpoB / PBP1B activator / peptidoglycan synthesis
Function / homologyABC-type transport auxiliary lipoprotein component / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsJean, N.L. / Egan, A.J.F. / Koumoutsi, A. / Bougault, C.M. / Typas, A. / Vollmer, W. / Simorre, J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Outer-membrane lipoprotein LpoB spans the periplasm to stimulate the peptidoglycan synthase PBP1B.
Authors: Egan, A.J. / Jean, N.L. / Koumoutsi, A. / Bougault, C.M. / Biboy, J. / Sassine, J. / Solovyova, A.S. / Breukink, E. / Typas, A. / Vollmer, W. / Simorre, J.P.
History
DepositionDec 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 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: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)20,7701
Polymers20,7701
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 / 750structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Penicillin-binding protein activator LpoB / PBP activator LpoB


Mass: 20770.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ycfM, lpoB, ECDH10B_1177 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1XA15

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Ensemble of 20 NMR structures of E. coli LpoB after refinement in water
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CO
1413D BEST-HN(CA)CB
1513D BEST-HN(CO)CACB
1613D HN(COCA)N(H)
1712D Pro-HN(COCAN)
1812D Pro-iHN(CAN)
1912D 1H-13C HSQC aliphatic
11012D 1H-13C HSQC aromatic
11112D methyl 1H-13C-CT-HSQC
11212D 1H-15N HMQC optimized for His sidechains
11313D (H)CCH-TOCSY
11413D H(CCO)NH
11513D C(CO)NH
11613D 1H-15N NOESY
11713D 1H-13C NOESY aliphatic
11813D 1H-13C NOESY aromatic
11913D methyl 1H-13C NOESY
1201Heteronuclear 1H-15N NOE

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] LpoB, 100.0 mM CH3COOH/CH3COONa buffer, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMLpoB-1[U-100% 13C; U-100% 15N]1
100.0 mMCH3COOH/CH3COONa buffer-21
Sample conditionsIonic strength: 0.100 / pH: 5.000 / Pressure: 1.000 atm / Temperature: 308.000 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian vnmrsVarianvnmrs8001
Varian vnmrsVarianvnmrs6002
Bruker US2BrukerUS29503

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr Analysis2.2CCPNdata analysis
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
Unio10'2.0.2Torsten Herrmannstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 5138 / NOE intraresidue total count: 1255 / NOE long range total count: 1240 / NOE medium range total count: 575 / NOE sequential total count: 779 / Protein phi angle constraints total count: 124 / Protein psi angle constraints total count: 124
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 750 / Conformers submitted total number: 20

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