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- PDB-2k3p: Solution structure of the C-terminal domain (TUSP1-C) of the egg ... -

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Basic information

Entry
Database: PDB / ID: 2k3p
TitleSolution structure of the C-terminal domain (TUSP1-C) of the egg case silk from Nephila antipodiana
ComponentsTuSp1
KeywordsSTRUCTURAL PROTEIN / EGGCASE SILK
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Spidroin domain, C-terminal 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 / Arc Repressor Mutant, subunit A / 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.
CitationJournal: 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.
History
DepositionMay 15, 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 / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)15,8771
Polymers15,8771
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


Mass: 15876.822 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 305-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila antipodiana (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1I128

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D CCH-TOCSY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1614D NOESY

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Sample preparation

DetailsContents: 1.5 mM [U-99% 13C; U-99% 15N] TUSP1-C, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: TUSP1-C / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 5 / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker DPX / Manufacturer: Bruker / Model: DPX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructural calculation
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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