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- PDB-8gs7: SOLUTION NMR STRUCTURE OF N-TERMINAL DOMAIN OF TRICONEPHILA CLAVI... -

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Entry
Database: PDB / ID: 8gs7
TitleSOLUTION NMR STRUCTURE OF N-TERMINAL DOMAIN OF TRICONEPHILA CLAVIPES MAJOR AMPULLATE SPIDROIN 2
ComponentsMajor ampullate spidroin 2 variant 3
KeywordsSTRUCTURAL PROTEIN / DRAGLINE SPIDER SILK / SPIDER SILK ASSEMBLY / PH REGULATION
Function / homologySpidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Major ampullate spidroin 2 variant 3
Function and homology information
Biological speciesTrichonephila clavipes (spider)
MethodSOLUTION NMR / molecular dynamics
AuthorsOktaviani, N.A. / Malay, A.D. / Matsugami, A. / Hayashi, F. / Numata, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER1602 Japan
Japan Science and TechnologyImpulsing paradigm through disruptive technology program Japan
CitationJournal: Biomacromolecules / Year: 2023
Title: Unusual p K a Values Mediate the Self-Assembly of Spider Dragline Silk Proteins.
Authors: Oktaviani, N.A. / Malay, A.D. / Matsugami, A. / Hayashi, F. / Numata, K.
History
DepositionSep 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major ampullate spidroin 2 variant 3


Theoretical massNumber of molelcules
Total (without water)14,4721
Polymers14,4721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Major ampullate spidroin 2 variant 3


Mass: 14472.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichonephila clavipes (spider) / Gene: MaSp2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S2B4G5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC; 2D 1H-13C HSQC ALIPHATIC; 2D 1H-13C HSQC AROMATIC; 3D CBCA(CO)NH; 3D HN(CA)CB; 3D HNCO; 3D HN(CA)CO; 3D HNHAHB; 3D HBHA(CO)NH; 3D 1H-13C NOESY ALIPHATIC; 3D 1H-15N NOESY; 3D H(CCO)NH; 3D (H)CCH-TOCSY; 2D HB(CBCG)CD(HD); 2D HB(CBCGCD) CE(HE)
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
181isotropic13D HNCO
171isotropic13D HN(CA)CO
161isotropic13D HBHA(CO)NH
191isotropic13D HNHAHB
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-15N NOESY
1121isotropic13D H(CCO)NH
1131isotropic13D (H)CCH-TOCSY
1141isotropic12D HB(CBCGCD)CE(HE)
1151isotropic12D HB(CBCG)CD(HD)
NMR detailsText: NULL

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Sample preparation

DetailsType: fibrous protein
Contents: 1 mM [U-13C; U-15N] N-terminal domain of NTD MaSp2 from Triconephila clavipes, 0.1 mM DSS, 10 % v/v [U-100% 2H] D2O, 300 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O
Label: 13C_15N NTD MaSp2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMN-terminal domain of NTD MaSp2 from Triconephila clavipes[U-13C; U-15N]1
0.1 mMDSSnatural abundance1
10 % v/vD2O[U-100% 2H]1
300 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 300 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee, Tonelli, Markleychemical shift assignment
MagRO-NMRViewKobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, Yokoyamachemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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