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- PDB-2n8x: Solution structure of LptE from Pseudomonas Aerigunosa -

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Basic information

Entry
Database: PDB / ID: 2n8x
TitleSolution structure of LptE from Pseudomonas Aerigunosa
ComponentsLPS-assembly lipoprotein LptE
KeywordsLIPID BINDING PROTEIN / LPS biosynthesis
Function / homology
Function and homology information


lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / lipopolysaccharide binding / cell outer membrane
Similarity search - Function
Lipoprotein like domain / Lipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsMoehle, K. / Kocherla, H. / Jurt, S. / Robinson, J. / Zerbe, O. / Zerbe, K. / Bacsa, B.
CitationJournal: Biochemistry / Year: 2016
Title: Solution Structure and Dynamics of LptE from Pseudomonas aeruginosa.
Authors: Moehle, K. / Kocherla, H. / Bacsa, B. / Jurt, S. / Zerbe, K. / Robinson, J.A. / Zerbe, O.
History
DepositionOct 28, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Structure summary
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPS-assembly lipoprotein LptE


Theoretical massNumber of molelcules
Total (without water)18,4111
Polymers18,4111
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 LPS-assembly lipoprotein LptE


Mass: 18411.461 Da / Num. of mol.: 1 / Fragment: residues 21-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lptE, PA3988, rlpB / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9HX32

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR structure of LptE from Pseudomonas Aerigunosa
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1433D HNCO
1533D HN(CA)CB
1633D HN(COCA)CB
1723D (H)CCH-TOCSY
1823D 1H-15N NOESY
1923D 1H-13C NOESY aliphatic
11023D 1H-13C NOESY aromatic
11123D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM 2H,13C,15N-labeled protein, 50 mM sodium phosphate, 25 mM sodium chloride, 20 mM CHAPS, 90% H2O/10% D2O90% H2O/10% D2O
20.35 mM 13C,15N-labeled protein, 50 mM sodium phosphate, 25 mM sodium chloride, 20 mM CHAPS, 90% H2O/10% D2O90% H2O/10% D2O
350 mM sodium phosphate, 25 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate-11
25 mMsodium chloride-21
20 mMCHAPS-31
50 mMsodium phosphate-42
25 mMsodium chloride-52
20 mMCHAPS-62
50 mMsodium phosphate-73
25 mMsodium chloride-83
Sample conditionsIonic strength: 55 / pH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2-1.39Schwieters, Kuszewski, Tjandra and Clorerefinement
CARA1.9Keller and Wuthrichchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: protocol incorporating RDCs as sample protocol from NIH package
NMR constraintsNOE constraints total: 1913 / NOE intraresidue total count: 521 / NOE long range total count: 475 / NOE medium range total count: 300 / NOE sequential total count: 617
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.29 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.94 °
NMR ensemble rmsDistance rms dev: 0.039 Å / Distance rms dev error: 0.003 Å

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