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- PDB-2jpo: NMR structure of Antheraea polyphemus pheromone-binding protein 1... -

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Basic information

Entry
Database: PDB / ID: 2jpo
TitleNMR structure of Antheraea polyphemus pheromone-binding protein 1 at pH 4.5
ComponentsPheromone-binding protein
KeywordsTRANSPORT PROTEIN / insect odorant-binding protein / pH-dependent conformation / helix insertion
Function / homology
Function and homology information


response to pheromone / pheromone binding
Similarity search - Function
Odorant/pheromone binding protein, Lepidoptera / Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pheromone-binding protein
Similarity search - Component
Biological speciesAntheraea polyphemus (polyphemus moth)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
Model detailsThe structure determination of ApolPBP1 was performed at pH 4.5 in the absense of signals from the ...The structure determination of ApolPBP1 was performed at pH 4.5 in the absense of signals from the alternate high pH conformation and contains a helix formed by the C-terminal dodecapeptide in the binding site.
AuthorsDamberger, F.F. / Wuthrich, K. / Leal, W.S. / Ishida, Y.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural Basis of Ligand Binding and Release in Insect Pheromone-Binding Proteins: NMR Structure of Antheraea polyphemus PBP1 at pH 4.5
Authors: Damberger, F.F. / Ishida, Y. / Leal, W.S. / Wuthrich, K.
#1: Journal: J.Biomol.NMR / Year: 2002
Title: Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS
Authors: Herrmann, T. / Guntert, P. / Wuthrich, K.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Protein NMR structure determination with automated NOE assignment using the new software candid and the torsion angle dynamics algorithm DYANA
Authors: Herrmann, T. / Guntert, P. / Wuthrich, K.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: Torsion angle dynamics for NMR structure calculation with the new program DYANA
Authors: Guntert, P. / Mumenthaler, C. / Wuthrich, K.
#4: Journal: J.Biomol.NMR / Year: 1996
Title: The new program opal for molecular dynamics simulations and energy refinement of biological macromolecules
Authors: Luginbuhl, P. / Guntert, P. / Billeter, M. / Wuthrich, K.
#5: Journal: Comput.Phys.Commun. / Year: 2000
Title: Point-centered domain decomposition for parallel molecular dynamics simulation
Authors: Koradi, R. / Billeter, M. / Guntert, P.
#6: Journal: CARA TUTORIAL / Year: 2004
Title: The computer-aided resonance assignment tutorial
Authors: Keller, R.
History
DepositionMay 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Derived calculations
Remark 650 HELIX DETERMINATION METHOD: KAPSCH AND SANDER APPLIED TO MEAN BACKBONE COORDINATES DERIVED FROM ... HELIX DETERMINATION METHOD: KAPSCH AND SANDER APPLIED TO MEAN BACKBONE COORDINATES DERIVED FROM ALIGNING BACKBONE HEAVY ATOMS OF RESIDUES 10-142.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pheromone-binding protein


Theoretical massNumber of molelcules
Total (without water)15,8021
Polymers15,8021
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 / 80target function
RepresentativeModel #1

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Components

#1: Protein Pheromone-binding protein / PBP


Mass: 15802.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Antheraea polyphemus (polyphemus moth) / Production host: Escherichia coli (E. coli) / References: UniProt: P20797

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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 CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
11313D (H)CCH-COSY
11413D HN(CA)CO
115115N- RESOLVED
11611H,1H TOCSY
11713D 15N- SEPARATED NOESY
11813D 13C- SEPARATED NOESY
NMR detailsText: TWO 13C-RESOLVED NOESY SPECTRA WERE MEASURED, ONE WITH THE 13C CARRIER CENTERED AT 35 PPM (ALIPHATICS), AND THE OTHER WITH THE CARRIER AT 125 PPM (AROMATICS). ALL PROTONS WERE EXCITED AND ...Text: TWO 13C-RESOLVED NOESY SPECTRA WERE MEASURED, ONE WITH THE 13C CARRIER CENTERED AT 35 PPM (ALIPHATICS), AND THE OTHER WITH THE CARRIER AT 125 PPM (AROMATICS). ALL PROTONS WERE EXCITED AND DECOUPLED WITH A REFOCUSSING 180 IN THE NOE DIMENSION, WHERE AS BROADBAND 13C-DECOUPLING WAS ONLY APPLIED TO ONE OF THE TWO CLASSES OF 1H DURING ACQUISITION.

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Sample preparation

DetailsContents: 0.9 MM [U-99% 13C; U-99% 15N] APOLPBP1, 2MM NAN3, 50MM PHOSPHATE BUFFER, 95% H2O/5% D2O
SampleConc.: 0.9 mM / Component: entity / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.05 / pH: 4.50 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker DRXBrukerDRX7502
Bruker DRXBrukerDRX5003
Bruker DRXBrukerDRX6004

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Processing

NMR software
NameVersionDeveloperClassification
OPALP1.2LUGINBUHL, GUNTERT, BILLETER, AND WUTHRICHrefinement
CARA1.8structure solution
ATNOS/CANDID1.2structure solution
DYANA1.0.3structure solution
MOLMOL2.2Kstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: SIMULATED ANNEALING USING TORSION ANGLE DYNAMICS FOLLOWED BY REFINEMENT IN A WATER BATH
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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