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- PDB-7dfe: NMR structure of TuSp2-RP -

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Basic information

Entry
Database: PDB / ID: 7dfe
TitleNMR structure of TuSp2-RP
ComponentsB6 protein
KeywordsPROTEIN FIBRIL / Spidroin / TuSp2 / Eggcase silk
Function / homologyTubuliform egg casing silk strands structural domain / Tubuliform egg casing silk strands structural domain / Spidroin, repetitive domain / B6 protein
Function and homology information
Biological speciesNephila antipodiana (spider)
MethodSOLUTION NMR / molecular dynamics
AuthorsLin, Z. / Fan, T. / Fan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21974093 China
Citation
Journal: Biomol.Nmr Assign. / Year: 2021
Title: 1H, 15N and 13C resonance assignments of a repetitive domain of tubuliform spidroin 2
Authors: Fan, T. / Zhang, Y. / Fan, J.S. / Yuan, W. / Lin, Z.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Critical role of minor eggcase silk component in promoting spidroin chain alignment and strong fiber formation.
Authors: Fan, T. / Qin, R. / Zhang, Y. / Wang, J. / Fan, J.S. / Bai, X. / Yuan, W. / Huang, W. / Shi, S. / Su, X.C. / Yang, D. / Lin, Z.
History
DepositionNov 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
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.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / 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: B6 protein
B: B6 protein


Theoretical massNumber of molelcules
Total (without water)30,6812
Polymers30,6812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2420 Å2
ΔGint-15 kcal/mol
Surface area15140 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein B6 protein


Mass: 15340.556 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila antipodiana (spider) / Tissue: tubuliform gland / Production host: Escherichia coli (E. coli) / References: UniProt: A5Y0M2

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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
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D HNCA
151isotropic13D HN(CO)CA
181isotropic13D CCH TOCSY
191isotropic14D 13C,15N-edited NOESY
1101isotropic13D 13C, 15N-filtered NOESY

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-99% 13C; U-99% 15N] TuSp2-RP, 95% H2O/5% D2O
Label: 15N,13C / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.6 mM / Component: TuSp2-RP / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0 mM / Ionic strength err: 0.01 / Label: 15N 13C / pH: 5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker Bruker Avance / Manufacturer: Bruker / Model: Bruker Avance / Field strength: 800 MHz / Details: Bruker Avance 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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