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- PDB-2jms: NMR Structure of En-6 pheromone from the Antarctic Ciliate Euplot... -

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Basic information

Entry
Database: PDB / ID: 2jms
TitleNMR Structure of En-6 pheromone from the Antarctic Ciliate Euplotes nobilii
ComponentsPheromone En-6
KeywordsSIGNALING PROTEIN / PROTEIN
Function / homologyPheromone ER-1 - #40 / Pheromone ER-1 / Up-down Bundle / Mainly Alpha / Pheromone En-6
Function and homology information
Biological speciesEuplotes nobilii (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, energy minimization
AuthorsPedrini, B. / Placzek, W.J. / Koculi, E. / Alimenti, C. / LaTerza, A. / Luporini, P. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Cold-adaptation in Sea-water-borne Signal Proteins: Sequence and NMR Structure of the Pheromone En-6 from the Antarctic Ciliate Euplotes nobilii
Authors: Pedrini, B. / Placzek, W.J. / Koculi, E. / Alimenti, C. / LaTerza, A. / Luporini, P. / Wuthrich, K.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 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
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pheromone En-6


Theoretical massNumber of molelcules
Total (without water)7,0331
Polymers7,0331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Pheromone En-6


Mass: 7033.396 Da / Num. of mol.: 1 / Fragment: residues 32-94 / Source method: isolated from a natural source / Source: (natural) Euplotes nobilii (eukaryote) / Strain: AC-4 / References: UniProt: A0FKY4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H NOESY
1531D 1H

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM En-6, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM En-6, 20 mM sodium phosphate, 100% D2O100% D2O
31 mM En-6, 20 mM sodium phosphate, 1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMEn-61
20 mMsodium phosphate1
1 mMEn-62
20 mMsodium phosphate2
1 mMEn-63
20 mMsodium phosphate3
1 mMDSS3
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 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
CARA1.5.3Keller and Wuthrichchemical shift assignment
XwinNMRBruker Biospincollection
ATNOS/CANDID1.1Herrmann, Guntert and Wuthrichpeak assignment
ATNOS/CANDID1.1Herrmann, Guntert and Wuthrichstructure solution
CYANA1.2Guntert, Mumenthaler and Wuthrichpeak picking
OPALpKoradi, Billeter and Guntertrefinement
RefinementMethod: torsion angle dynamics, energy minimization / Software ordinal: 1
Details: CYANA-1.2, used within the 7-cycle iterated ATNOS/CANDID/CYANA procedure and OPALp, applied to the final conformer bundle from ATNOS/CANDID/CYANA
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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