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- PDB-6tv5: NMR structure of N-terminal domain from A. argentata tubuliform s... -

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Basic information

Entry
Database: PDB / ID: 6tv5
TitleNMR structure of N-terminal domain from A. argentata tubuliform spidroin (TuSp) at pH 5.5
ComponentsTubuliform spidroin 1
KeywordsSTRUCTURAL PROTEIN / Spidroin / N-terminal domain / spidersilk
Function / homologyTubuliform egg casing silk strands structural domain / Tubuliform egg casing silk strands structural domain / Spidroin, repetitive domain / Spidroin, N-terminal domain superfamily / Tubuliform spidroin 1
Function and homology information
Biological speciesArgiope argentata (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFridmanis, J. / Jaudzems, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other government1.1.1.1/18/A/004 Latvia
CitationJournal: Front Mol Biosci / Year: 2022
Title: Solution Structure of Tubuliform Spidroin N-Terminal Domain and Implications for pH Dependent Dimerization.
Authors: Sede, M. / Fridmanis, J. / Otikovs, M. / Johansson, J. / Rising, A. / Kronqvist, N. / Jaudzems, K.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubuliform spidroin 1
B: Tubuliform spidroin 1


Theoretical massNumber of molelcules
Total (without water)28,1112
Polymers28,1112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, T1, T2 relaxation assay
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3180 Å2
ΔGint-20 kcal/mol
Surface area12030 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Tubuliform spidroin 1


Mass: 14055.446 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argiope argentata (spider) / Gene: TuSp1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2YSJ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic13D CBCA(CO)NH
151isotropic13D HNHA
161isotropic13D HNCA
171isotropic13D HN(CA)CO
181isotropic13D HNCO
191isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 20 mM NA sodium chloride, 20 mM [U-99% 2H] acetic acid, 2 mM [U-13C; U-15N] Tubuliform protein N-terminal domain, 0.03 % NA sodium azide, 1 mM NA EDTA, 95% H2O/5% D2O
Label: 15N_13C sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium chlorideNA1
20 mMacetic acid[U-99% 2H]1
2 mMTubuliform protein N-terminal domain[U-13C; U-15N]1
0.03 %sodium azideNA1
1 mMEDTANA1
Sample conditionsIonic strength: 0.0285 M / Label: Dimer_solution / pH: 5.5 / PH err: 0.1 / Pressure: AMBIENT atm / Temperature: 298 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4Keller and Wuthrichchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CANDID2.2Herrmann, Guntert and Wuthrichpeak picking
TopSpin4.0.6Bruker Biospinprocessing
CANDIDHerrmann, Guntert and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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