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- PDB-2jnf: Solution structure of fly troponin C, isoform F1 -

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Basic information

Entry
Database: PDB / ID: 2jnf
TitleSolution structure of fly troponin C, isoform F1
ComponentsTroponin C
KeywordsMETAL BINDING PROTEIN / Stretch Activated Muscle Contraction / Troponin C / EF-hand / lethocerus indicus
Function / homology
Function and homology information


enzyme regulator activity / calcium ion binding
Similarity search - Function
EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesLethocerus indicus (insect)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsDe Nicola, G.F. / Bullard, B. / Pastore, A.
CitationJournal: Structure / Year: 2007
Title: The structure of lethocerus troponin C: insights into the mechanism of stretch activation in muscles
Authors: De Nicola, G. / Burkart, C. / Qiu, F. / Agianian, B. / Labeit, S. / Martin, S. / Bullard, B. / Pastore, A.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Troponin C


Theoretical massNumber of molelcules
Total (without water)17,5891
Polymers17,5891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Troponin C /


Mass: 17589.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lethocerus indicus (insect) / Gene: tnC4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q868D4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D 1H-15N NOESY
1423D 1H-13C NOESY
1523D HN(COCA)CB
1623D HNCA
1723D HN(CA)CB
1823D CBCA(CO)NH
1923D HNCO
11013D 1H-15N TOCSY
11123D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-99% 15N] muscle protein, 90% H2O, 10% D2O90% H2O/10% D2O
20.7 mM [U-99% 13C; U-99% 15N] muscle protein, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMmuscle protein[U-99% 15N]1
0.7 mMmuscle protein[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
XEASYBartels et al.data analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1 / Details: water refinement
NMR constraintsNOE constraints total: 3840 / NOE intraresidue total count: 1578 / NOE long range total count: 842 / NOE medium range total count: 573 / NOE sequential total count: 840
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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