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- PDB-7but: N-terminal domain (NTD) Solution structure of aciniform spidroin ... -

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Basic information

Entry
Database: PDB / ID: 7but
TitleN-terminal domain (NTD) Solution structure of aciniform spidroin (AcSpN) from Nephila antipodiana.
ComponentsAciniform Spidroin
KeywordsSTRUCTURAL PROTEIN / N-terminal domain / spidroin
Biological speciesNephila antipodiana (spider)
MethodSOLUTION NMR / simulated annealing
AuthorsFan, J.S. / Yang, D.W.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)Tier1-R154000A50114 Singapore
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Basis of Oligomerization of N-Terminal Domain of Spider Aciniform Silk Protein.
Authors: Chakraborty, R. / Fan, J.S. / Lai, C.C. / Raghuvamsi, P.V. / Chee, P.X. / Anand, G.S. / Yang, D.
History
DepositionApr 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aciniform Spidroin


Theoretical massNumber of molelcules
Total (without water)15,3181
Polymers15,3181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aciniform Spidroin


Mass: 15318.378 Da / Num. of mol.: 1 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila antipodiana (spider) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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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
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D (H)CCH-TOCSY
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM [U-100% 13C; U-100% 15N] NTD, 95% H2O/5% D2O / Label: CN_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: NTD / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 500 mM / Ionic strength err: 1 / Label: con_1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.53Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.53Schwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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