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- PDB-2b1u: Solution structure of Calmodulin-like Skin Protein C terminal domain -

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Basic information

Entry
Database: PDB / ID: 2b1u
TitleSolution structure of Calmodulin-like Skin Protein C terminal domain
ComponentsCalmodulin-like protein 5
KeywordsMETAL BINDING PROTEIN / CLSP / Calmodulin-like skin protein / Solution structure / Backbone dynamic / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / epidermis development / enzyme regulator activity / microtubule cytoskeleton organization / ficolin-1-rich granule lumen / calcium ion binding / Neutrophil degranulation / signal transduction / extracellular region / cytoplasm
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
Calmodulin-like protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, restrained energy minimization
AuthorsBabini, E. / Bertini, I. / Capozzi, F. / Chirivino, E. / Luchinat, C. / Structural Proteomics in Europe (SPINE)
CitationJournal: Structure / Year: 2006
Title: A Structural and Dynamic Characterization of the EF-Hand Protein CLSP.
Authors: Babini, E. / Bertini, I. / Capozzi, F. / Chirivino, E. / Luchinat, C.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 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-like protein 5


Theoretical massNumber of molelcules
Total (without water)7,9701
Polymers7,9701
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 / 400target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Calmodulin-like protein 5 / Calmodulin-like skin protein


Mass: 7969.740 Da / Num. of mol.: 1 / Fragment: C terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALML5 / Plasmid: pQE30Xa / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: Q9NZT1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
1413D 15N-separated TOCSY
151HNHA

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Sample preparation

DetailsContents: 2mM 15N protein sample / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
CARA1.2Keller, R.data analysis
CYANA1.2Herrmann, T., Guntert, P., and Wuthrich, Kstructure solution
Amber5refinement
RefinementMethod: torsion angle dynamics, simulated annealing, restrained energy minimization
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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