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- PDB-5lah: NMR structure of the sea anemone peptide tau-AnmTx Ueq 12-1 with ... -

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Basic information

Entry
Database: PDB / ID: 5lah
TitleNMR structure of the sea anemone peptide tau-AnmTx Ueq 12-1 with an uncommon fold
Componentstau-AnmTx Ueq 12-1
KeywordsTOXIN / PROTEIN / sea anemone / antimicrobial peptide / TRPA1 potentiator / membrane protein
Function / homologytoxin activity / defense response to bacterium / extracellular region / Tau-AnmTx Ueq 12-1
Function and homology information
Biological speciesUrticina eques (sea anemone)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMineev, K.S. / Arseniev, A.S. / Andreev, Y.A. / Kozlov, S.A. / Logashina, Y.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation16-15-00167 Russian Federation
CitationJournal: Toxins / Year: 2017
Title: New Disulfide-Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating Properties
Authors: Logashina, Y.A. / Solstad, R.G. / Mineev, K.S. / Korolkova, Y.V. / Mosharova, I.V. / Dyachenko, I.A. / Palikov, V.A. / Palikova, Y.A. / Murashev, A.N. / Arseniev, A.S. / Kozlov, S.A. / ...Authors: Logashina, Y.A. / Solstad, R.G. / Mineev, K.S. / Korolkova, Y.V. / Mosharova, I.V. / Dyachenko, I.A. / Palikov, V.A. / Palikova, Y.A. / Murashev, A.N. / Arseniev, A.S. / Kozlov, S.A. / Stensvag, K. / Haug, T. / Andreev, Y.A.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tau-AnmTx Ueq 12-1


Theoretical massNumber of molelcules
Total (without water)4,8081
Polymers4,8081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3060 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide tau-AnmTx Ueq 12-1


Mass: 4808.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Urticina eques (sea anemone) / References: UniProt: C0HK26*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC
142isotropic12D 1H-13C HSQC
152isotropic12D 1H-1H NOESY
162isotropic12D 1H-1H TOCSY
172isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 95% H2O/5% D2Owater sample95% H2O/5% D2O
solution20.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMtau-AnmTx Ueq 12-1natural abundance1
1 mMsodium azidenatural abundance1
0.5 mMtau-AnmTx Ueq 12-1natural abundance2
1 mMsodium azidenatural abundance2
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 3.2 / PH err: 0.1 / Pressure: AMBIENT atm / Temperature: 303 K / Temperature err: 0.05

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.4Keller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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