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- PDB-6qjy: Solution NMR structure of a mutant major ampullate spidroin 1 N-t... -

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Basic information

Entry
Database: PDB / ID: 6qjy
TitleSolution NMR structure of a mutant major ampullate spidroin 1 N-terminal domain
ComponentsMajor ampullate spidroin 1
KeywordsSTRUCTURAL PROTEIN / spider silk hydrophobic core methionine
Function / homologySpidroin, N-terminal domain / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha / identical protein binding / Major ampullate spidroin 1
Function and homology information
Biological speciesEuprosthenops australis (spider)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS ONFORMERS, NUMBER CALCULATED : NULL
AuthorsGoretzki, B. / Heiby, J. / Neuweiler, H. / Hellmich, U.A.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
United States
Germany
CitationJournal: Nat Commun / Year: 2019
Title: Solution NMR structure of a mutant major ampullate spidroin 1 N-terminal domain
Authors: Heiby, J.H. / Goretzki, B. / Johnson, C.M. / Hellmich, U.A. / Neuweiler, H.
History
DepositionJan 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major ampullate spidroin 1


Theoretical massNumber of molelcules
Total (without water)14,0751
Polymers14,0751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Size exclusion chromatography and multi-angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major ampullate spidroin 1


Mass: 14075.485 Da / Num. of mol.: 1 / Mutation: M20L, M24L, M41L, M48L, M77L, M101L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Euprosthenops australis (spider) / Gene: MaSp1 / Plasmid: pRSET A / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q05H60

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 13C(ali)-NOESY-HSQC
1101isotropic12D 13C HSQC
121isotropic23D 15N-NOESY-HSQC
1111isotropic22D 15N HSQC
131isotropic23D HNCAO
141isotropic23D HNCO
151isotropic23D HNCA
191isotropic23D HN(CA)CB
181isotropic23D CBCA(CO)NH
171isotropic23D HBHA(CO)NH
161isotropic23D H(CCO)NH
1131isotropic23D H(CCO)NH
1121isotropic23D (H)CCH-TOCSY
1141isotropic23D (H)CCH-TOCSY
NMR detailsText: NULL

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] MaSp1 L6-NTD, 50 mM potassium phosphate, 200 mM sodium chloride, 100 uM DSS, 90% H2O/10% D2O
Label: 13C,15N_L6-NTD / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMMaSp1 L6-NTD[U-13C; U-15N]1
50 mMpotassium phosphatenatural abundance1
200 mMsodium chloridenatural abundance1
100 uMDSSnatural abundance1
Sample conditionsIonic strength: 200 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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
OPAL2.4.2Luginbuhl, Guntert, Billeter and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: TORSION ANGLE DYNAMICS ONFORMERS, NUMBER CALCULATED : NULL
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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