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- PDB-1tiz: Solution Structure of a Calmodulin-Like Calcium-Binding Domain fr... -

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Basic information

Entry
Database: PDB / ID: 1tiz
TitleSolution Structure of a Calmodulin-Like Calcium-Binding Domain from Arabidopsis thaliana
Componentscalmodulin-related protein, putative
KeywordsCalcium-Binding Protein / helix-turn-helix / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
: / EF hand / 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 / 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
Probable calcium-binding protein CML34
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsSong, J. / Zhao, Q. / Thao, S. / Frederick, R.O. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biomol.NMR / Year: 2004
Title: Letter to the Editor: Solution structure of a calmodulin-like calcium-binding domain from Arabidopsis thaliana
Authors: Song, J. / Zhao, Q. / Thao, S. / Frederick, R.O. / Markley, J.L.
History
DepositionJun 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: calmodulin-related protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7421
Polymers7,7421
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein calmodulin-related protein, putative


Mass: 7741.602 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SRP5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D techniques.

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Sample preparation

DetailsContents: 5 mM DTT, 20 mM Bis-Tris, 5mM Ca2+, 1mM DSS, 0.02% NaN3, 1 mM protein
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.4 / Pressure: 1 atm / Temperature: 298.2 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
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionClassification
XwinNMR3.2collection
NMRPipe2.1processing
Sparky3.72data analysis
CYANA1.0.5structure solution
XPLOR-NIH2.0.6refinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: The structure was first calculated using torsion angle dynamics, and later refined using simulated annealing and molecular dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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