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- PDB-2k3o: Solution structure of the type 2 repetitive domain (TUSP1-RP2) of... -

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Basic information

Entry
Database: PDB / ID: 2k3o
TitleSolution structure of the type 2 repetitive domain (TUSP1-RP2) of the egg case silk from Nephila Antipodiana
ComponentsTuSp1
KeywordsSTRUCTURAL PROTEIN / HELIX
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Spidroin, repetitive domain / Tubuliform egg casing silk strands structural domain / Tubuliform egg casing silk strands structural domain / Spidroin, C-terminal / Spidroin, repetitive domain / Major ampullate spidroin 1 and 2 / Spidroin, C-terminal domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesNephila antipodiana (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLin, Z. / Huang, W. / Fan, J. / Yang, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Solution structure of eggcase silk protein and its implications for silk fiber formation
Authors: Lin, Z. / Huang, W. / Zhang, J. / Fan, J.S. / Yang, D.
#1: Journal: To be Published
Title: Resonance Assignments of a Repeated Domain of the Egg Case Silk from Nephila Antipodiana
Authors: Lin, Z. / Huang, W. / Yang, D.
History
DepositionMay 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TuSp1


Theoretical massNumber of molelcules
Total (without water)11,9991
Polymers11,9991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TuSp1 / EGG CASE SILK


Mass: 11998.957 Da / Num. of mol.: 1 / Fragment: LAST REPEATED DOMAIN, RP2 (UNP residues 186-314)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila antipodiana (spider) / Gene: EGGCASE SILK GENE / Plasmid: PET-32A-DERIVED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q1I128

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-SEPARATED NOESY
1213D HNCA
1313D TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] TUSP1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: TUSP1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 290 K

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NMR measurement

NMR spectrometerType: BRUKER DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber7DAVID A. CASE, ET. AL.refinement
NMRPipe2004Frank Dagliastructure solution
NMRView5.2.2Bruce A. Johnsonstructure solution
CYANA1.05Peter Guntertstructure solution
RefinementMethod: torsion angle 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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