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- PDB-1oqp: STRUCTURE OF THE CA2+/C-TERMINAL DOMAIN OF CALTRACTIN IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1oqp
TitleSTRUCTURE OF THE CA2+/C-TERMINAL DOMAIN OF CALTRACTIN IN COMPLEX WITH THE CDC31P-BINDING DOMAIN FROM KAR1P
Components
  • Caltractin
  • Cell division control protein KAR1
KeywordsPROTEIN BINDING / protein-peptide complex / caltractin / KAR1P / calcium-binding
Function / homology
Function and homology information


half bridge of spindle pole body / inner dynein arm / spindle pole body duplication / karyogamy involved in conjugation with cellular fusion / dynein heavy chain binding / microtubule / cell division / calcium ion binding / endoplasmic reticulum
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 ...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
Caltractin / Cell division control protein KAR1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHu, H.T. / Chazin, W.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Unique Features in the C-terminal Domain Provide Caltractin with Target Specificity
Authors: Hu, H.T. / Chazin, W.J.
History
DepositionMar 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

Downloads & links

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Assembly

Deposited unit
A: Caltractin
B: Cell division control protein KAR1


Theoretical massNumber of molelcules
Total (without water)11,4792
Polymers11,4792
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 / 60structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein Caltractin / Centrin / 20 kDa calcium-binding protein


Mass: 8977.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: P05434
#2: Protein/peptide Cell division control protein KAR1


Mass: 2501.003 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide consists of the cdc31p-binding domain from Kar1p, residues 239-257, and has been chemically synthesized using solid phase F-Moc chemistry. The sequence is naturally found in ...Details: The peptide consists of the cdc31p-binding domain from Kar1p, residues 239-257, and has been chemically synthesized using solid phase F-Moc chemistry. The sequence is naturally found in Saccharomyces cerevisiae (baker's yeast).
References: UniProt: P11927

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1324D 13C-separated NOESY
1432D NOESY
1523D 13C-F1-edited, 13C-F3-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM CRC-C U-15N,13C; 1.2mM K19 unlabeled.5mM CaCl2, 25mM Tris, 50mM KCl, 90% H2O, 10% D2O
21mM CRC-C U-15N,13C; 1.2mM K19 unlabeled.5mM CaCl2, 25mM Tris, 50mM KCl, 100% D2O
31mM CRC-C unlabeled; 1.2 mM K19 unlabeled.5mM CaCl2, 25mM Tris, 50mM KCl, 90% H2O, 10% D2O
Sample conditionsIonic strength: 50mM KCl, 5mM CaCl2 / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Felix2000Accelrys, San Diego, CAprocessing
Felix2000Accelrys, San Diego, CAdata analysis
DYANA1.5Guntert, P., Mumenthaler, C. & Wuthrich, K.structure solution
Amber7Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham III, T.E., DeBolt, S., Ferguson, D., Seibel, G., Kollman, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1827 constraints, 1641 are NOE-derived distance constraints, 134 dihedral angle constraints, 52 distance constraints from hydrogen bonds.
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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