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- PDB-2ncp: NMR solution structure for the C-terminal domain of Tetrahymena T... -

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Basic information

Entry
Database: PDB / ID: 2ncp
TitleNMR solution structure for the C-terminal domain of Tetrahymena Tcb2 in the presence of calcium
Components25 kDa calcium-binding protein
KeywordsMETAL BINDING PROTEIN / calcium binding protein / EF hand / contractility / helical packing / cytoskeleton / TCB25
Function / homology
Function and homology information


regulation of presynaptic cytosolic calcium ion concentration / cell projection organization / regulation of long-term synaptic potentiation / calcium ion binding / dendrite / nucleus / cytosol
Similarity search - Function
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
25 kDa calcium-binding protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsFowler, A. / Kilpatrick, A.M.
Citation
Journal: Proteins / Year: 2016
Title: Solution NMR structures of the C-domain of Tetrahymena cytoskeletal protein Tcb2 reveal distinct calcium-induced structural rearrangements.
Authors: Kilpatrick, A.M. / Honts, J.E. / Sleister, H.M. / Fowler, C.A.
#1: Journal: Biomol.Nmr Assign. / Year: 2016
Title: Backbone and side-chain chemical shift assignments for the C-terminal domain of Tcb2, a cytoskeletal calcium-binding protein from Tetrahymena thermophila.
Authors: Kilpatrick, A.M. / Gurrola, T.E. / Sterner, R.C. / Sleister, H.M. / Honts, J.E. / Fowler, C.A.
History
DepositionApr 11, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 25 kDa calcium-binding protein


Theoretical massNumber of molelcules
Total (without water)11,5781
Polymers11,5781
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein 25 kDa calcium-binding protein / TCBP-25 / 10 kDa calcium-binding protein / TCBP-10


Mass: 11578.022 Da / Num. of mol.: 1 / Fragment: EF-hands 3 and 4, residues 117-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P09226

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D H(CCO)NH
1623D HCACO
1722D 1H-13C HMQC
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY
11033D 1H-15N NOESY
11142D 1H-1H COSY
11242D 1H-1H TOCSY
11342D 1H-1H NOESY
11422D (HB)CB(CGCD)HD
11522D (HB)CB(CGCDCE)HE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-98% 13C; U-98% 15N] Tcb2-C, 25 mM TRIS, 50 mM potassium chloride, 5 mM magnesium chloride, 1 mM EGTA, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM [U-98% 13C; U-98% 15N] Tcb2-C, 25 mM TRIS, 50 mM potassium chloride, 5 mM magnesium chloride, 1 mM EGTA, 5 mM calcium chloride, 100% D2O100% D2O
30.75 mM [U-98% 15N] Tcb2-C, 25 mM TRIS, 50 mM potassium chloride, 5 mM magnesium chloride, 1 mM EGTA, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
40.75 mM Tcb2-C, 25 mM TRIS, 50 mM potassium chloride, 5 mM magnesium chloride, 1 mM EGTA, 5 mM calcium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMTcb2-C-1[U-98% 13C; U-98% 15N]1
25 mMTRIS-21
50 mMpotassium chloride-31
5 mMmagnesium chloride-41
1 mMEGTA-51
5 mMcalcium chloride-61
0.75 mMTcb2-C-7[U-98% 13C; U-98% 15N]2
25 mMTRIS-82
50 mMpotassium chloride-92
5 mMmagnesium chloride-102
1 mMEGTA-112
5 mMcalcium chloride-122
0.75 mMTcb2-C-13[U-98% 15N]3
25 mMTRIS-143
50 mMpotassium chloride-153
5 mMmagnesium chloride-163
1 mMEGTA-173
5 mMcalcium chloride-183
0.75 mMTcb2-C-194
25 mMTRIS-204
50 mMpotassium chloride-214
5 mMmagnesium chloride-224
1 mMEGTA-234
5 mMcalcium chloride-244
Sample conditionsIonic strength: 0.05 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
VnmrJVariancollection
AnalysisCCPNpeak picking
AnalysisCCPNdata analysis
AnalysisCCPNchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1666 / NOE intraresidue total count: 447 / NOE long range total count: 484 / NOE medium range total count: 374 / NOE sequential total count: 361 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 96 / Protein psi angle constraints total count: 96
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.43 ° / Maximum upper distance constraint violation: 0.23 Å
NMR ensemble rmsDistance rms dev: 0.002 Å / Distance rms dev error: 0.0009 Å

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