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- PDB-2k2a: Solution Structure of the Apo C terminal domain of Lethocerus tro... -

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Basic information

Entry
Database: PDB / ID: 2k2a
TitleSolution Structure of the Apo C terminal domain of Lethocerus troponin C isoform F1
ComponentsTroponin C
KeywordsCONTRACTILE PROTEIN / calcium binding protein
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. / Kelly, G. / Bullard, B. / McCormick, J.
CitationJournal: Biochemistry / Year: 2010
Title: Solution structure of the Apo C-terminal domain of the Lethocerus F1 troponin C isoform.
Authors: De Nicola, G.F. / Martin, S. / Bullard, B. / Pastore, A.
History
DepositionMar 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.3Jun 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 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)7,8491
Polymers7,8491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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: 7849.483 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) / 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
3232D 1H-13C HSQC
1313D 1H-15N NOESY
2423D 1H-15N NOESY
2522D 1H-15N HSQC
3633D (H)CCH-TOCSY
3733D 1H-13C NOESY
3833D CBCA(CO)NH
3933D HN(CO)CA
31033D HN(CA)CB
11113D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMprotein[U-99% 15N]1
100 mMsodium chloride1
20 mMTRIS1
0.4 mMprotein[U-99% 15N]2
100 mMsodium chloride2
20 mMTRIS2
0.4 mMprotein[U-99% 13C; U-99% 15N]3
100 mMsodium chloride3
20 mMTRIS3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.8 ambient atm298 K
20.1 6.8 ambient atm288 K
30.1 6.8 ambient atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
VNMRVariancollection
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: the structure were refined by molecular dynamics simulation in water using Aria 1.2
NMR constraintsNOE constraints total: 1311 / NOE intraresidue total count: 632 / NOE long range total count: 251 / NOE medium range total count: 149 / NOE sequential total count: 279 / Protein psi angle constraints total count: 28
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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