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- PDB-1m39: Solution structure of the C-terminal fragment (F86-I165) of the h... -

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Basic information

Entry
Database: PDB / ID: 1m39
TitleSolution structure of the C-terminal fragment (F86-I165) of the human centrin 2 in calcium saturated form
ComponentsCaltractin, isoform 1
KeywordsCELL CYCLE / EF-hand
Function / homology
Function and homology information


XPC complex / 9+2 motile cilium / photoreceptor connecting cilium / heterotrimeric G-protein binding / transcription export complex 2 / nuclear pore nuclear basket / centriole replication / mRNA transport / SUMOylation of DNA damage response and repair proteins / Loss of Nlp from mitotic centrosomes ...XPC complex / 9+2 motile cilium / photoreceptor connecting cilium / heterotrimeric G-protein binding / transcription export complex 2 / nuclear pore nuclear basket / centriole replication / mRNA transport / SUMOylation of DNA damage response and repair proteins / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / ciliary basal body / regulation of cytokinesis / nucleotide-excision repair / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / Formation of Incision Complex in GG-NER / Regulation of PLK1 Activity at G2/M Transition / protein transport / apical part of cell / mitotic cell cycle / spermatogenesis / microtubule binding / cell division / centrosome / calcium ion binding / nucleoplasm / cytosol
Similarity search - Function
ATP-dependent RNA helicase DEAD-box, conserved site / 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 ...ATP-dependent RNA helicase DEAD-box, conserved site / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, restraint energy minimization
AuthorsMatei, E. / Miron, S. / Blouquit, Y. / Duchambon, P. / Durussel, P. / Cox, J.A. / Craescu, C.T.
CitationJournal: Biochemistry / Year: 2003
Title: C-terminal half of human centrin 2 behaves like a regulatory EF-hand domain
Authors: Matei, E. / Miron, S. / Blouquit, Y. / Duchambon, P. / Durussel, P. / Cox, J.A. / Craescu, C.T.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: Caltractin, isoform 1


Theoretical massNumber of molelcules
Total (without water)10,3911
Polymers10,3911
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)25 / 76structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Caltractin, isoform 1 / Centrin 2


Mass: 10390.689 Da / Num. of mol.: 1 / Fragment: C-terminus (Residues 84-172)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEN2 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41208

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: LC-HsCen2 M84-Y172; Tris d11 20 mM buffer;100 mM NaCl; 93% H2O, 7% D2O
Solvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 308 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 spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DGIII2000Accelrysstructure solution
DiscoverI2000Accelrysrefinement
RefinementMethod: distance geometry, restraint energy minimization / Software ordinal: 1
Details: The structure is based on 1103 NOE restraints, 35 hydrogen bond restraints and 103 dihedral restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 76 / Conformers submitted total number: 25

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