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- PDB-1eq1: NMR STRUCTURE OF AN EXCHANGEABLE APOLIPOPROTEIN-MANDUCA SEXTA APO... -

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Basic information

Entry
Database: PDB / ID: 1eq1
TitleNMR STRUCTURE OF AN EXCHANGEABLE APOLIPOPROTEIN-MANDUCA SEXTA APOLIPOPHORIN-III
ComponentsAPOLIPOPHORIN-III
KeywordsLIPID BINDING PROTEIN / Five helix-bundle / "helix-short helix-helix" recognition motif
Function / homology
Function and homology information


lipid transport / lipid binding / extracellular region
Similarity search - Function
Apolipophorin-III / Apolipophorin-III precursor (apoLp-III) / Apolipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesManduca sexta (tobacco hornworm)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, J. / Sykes, B.D. / Ryan, R.O.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural basis for the conformational adaptability of apolipophorin III, a helix-bundle exchangeable apolipoprotein
Authors: Wang, J. / Sykes, B.D. / Ryan, R.O.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Insight into Lipid Surface Recognition and Reversible Conformational Adaptation of an Exchangeable Apolipoprotein by Multidimensional Heteronuclear NMR Techniques
Authors: Wang, J. / Gagne, S.M. / Sykes, B.D. / Ryan, R.O.
History
DepositionMar 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPHORIN-III


Theoretical massNumber of molelcules
Total (without water)18,4091
Polymers18,4091
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)25 / 40structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #2closest to the average, fewest violations

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Components

#1: Protein APOLIPOPHORIN-III / APOLP-III


Mass: 18409.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INTACT EXCHANGEABLE APOLIPOPROTEIN / Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Production host: Escherichia coli (E. coli) / References: UniProt: P13276

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
141HNHA
1514D 13C-separated NOESY
1614D 13C/15N-separated NOESY

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Sample preparation

DetailsContents: 0.8-1.2 mM U-15N, 13C double labeld L-apoLp-III; 200 mM phosphate buffer, 0.5 mM NaN3, DSS
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.4 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
NMRPipeDelaglio, Garrettdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2365 restraints, including 2257 NOE-direvied distance restraints and 108 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average, fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 40 / Conformers submitted total number: 25

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