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- PDB-1v50: Solution structure of phosphorylated N-terminal fragment of S100C... -

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Basic information

Entry
Database: PDB / ID: 1v50
TitleSolution structure of phosphorylated N-terminal fragment of S100C/A11 protein
ComponentsCalgizzarin
KeywordsMETAL BINDING PROTEIN / ALPHA-HELIX
Function / homology
Function and homology information


cadherin binding involved in cell-cell adhesion / S100 protein binding / negative regulation of DNA replication / positive regulation of smooth muscle cell migration / ruffle / adherens junction / calcium-dependent protein binding / secretory granule lumen / negative regulation of cell population proliferation / calcium ion binding ...cadherin binding involved in cell-cell adhesion / S100 protein binding / negative regulation of DNA replication / positive regulation of smooth muscle cell migration / ruffle / adherens junction / calcium-dependent protein binding / secretory granule lumen / negative regulation of cell population proliferation / calcium ion binding / Neutrophil degranulation / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm
Similarity search - Function
Protein S100-A11 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Protein S100-A11 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / 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
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, simulated annealing
Model type detailsminimized average
AuthorsKouno, T. / Mizuguchi, M. / Sakaguchi, M. / Makino, E. / Huh, N. / Kawano, K.
CitationJournal: Peptide Science / Year: 2003
Title: Study on structure-activity relationship between the N-terminal region of S100C protein and its function
Authors: Kouno, T. / Mizuguchi, M. / Sakaguchi, M. / Makino, E. / Huh, N. / Kawano, K.
History
DepositionNov 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: Calgizzarin


Theoretical massNumber of molelcules
Total (without water)2,1611
Polymers2,1611
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Calgizzarin / S100C protein / MLN 70 / S100C/A11


Mass: 2161.392 Da / Num. of mol.: 1 / Fragment: N-terminal fragment / Source method: obtained synthetically
Details: The sequence of the peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human)
References: UniProt: P31949

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM peptide, 20mM phosphate buffer NA, 5mM dithiothreitol, 50% H2O, 50% trifluoroethanol-d350% H2O, 50% trifluoroethanol-d3
22.0mM peptide, 20mM phosphate buffer NA, 5mM dithiothreitol, 50% D2O, 50% trifluoroethanol-d350% D2O, 50% trifluoroethanol-d3
Sample conditionsIonic strength: 0.12 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
PIPP4.3.2Garrettdata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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