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- PDB-2jnt: Structure of Bombyx mori Chemosensory Protein 1 in Solution -

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Basic information

Entry
Database: PDB / ID: 2jnt
TitleStructure of Bombyx mori Chemosensory Protein 1 in Solution
ComponentsChemosensory protein CSP1
KeywordsLIGAND BINDING PROTEIN / BmorCSP1 / CSP1
Function / homologyAntennal chemosensory protein a6 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 superfamily / Insect pheromone-binding family, A10/OS-D / Orthogonal Bundle / Mainly Alpha / Chemosensory protein 4
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodSOLUTION NMR / simulated annealing
AuthorsJansen, S. / Zidek, L. / Chmelik, J. / Novak, P. / Padrta, P. / Picimbon, J. / Lofstedt, C. / Sklenar, V.
CitationJournal: Arch.Insect Biochem.Physiol. / Year: 2007
Title: Structure of Bombyx mori chemosensory protein 1 in solution
Authors: Jansen, S. / Chmelik, J. / Zidek, L. / Padrta, P. / Novak, P. / Zdrahal, Z. / Picimbon, J.-F. / Lofstedt, C. / Sklenar, V.
History
DepositionFeb 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemosensory protein CSP1


Theoretical massNumber of molelcules
Total (without water)12,5581
Polymers12,5581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 750structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chemosensory protein CSP1 / Chemosensory protein 4 / Hypothetical protein


Mass: 12558.267 Da / Num. of mol.: 1 / Fragment: sequence database residues 20-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MMK7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H15N HSQC
121HNCA
131HN(CO)CA
141HN(CA)CB
151CBCA(CO)NH
161(H)CCH TOCSY
17113C15N edited NOESY
181HNCO
191(H)CCH TOCSY
110113C15N edited NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-95% 13C; U-90% 15N] chemosensory protein 1, 20 mM sodium phosphate, 0.05 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMchemosensory protein 1[U-95% 13C; U-90% 15N]1
20 mMsodium phosphate1
0.05 mMsodium azide1
Sample conditionspH: 6.0 / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddarddata analysis
ARIA2.0aLinge, O'Donoghue and Nilgesstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA2.0aLinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 750 / Conformers submitted total number: 10

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