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- PDB-2cxj: 3D Solution Structure of S100A13 -

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Basic information

Entry
Database: PDB / ID: 2cxj
Title3D Solution Structure of S100A13
ComponentsS100 calcium-binding protein A13
KeywordsMETAL BINDING PROTEIN / S100A13 / solution / FGF / non-classical secretion / calcium
Function / homology
Function and homology information


positive regulation of interleukin-1 alpha production / RAGE receptor binding / fibroblast growth factor binding / positive regulation of cytokine production / calcium-dependent protein binding / protein transport / regulation of cell shape / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / copper ion binding ...positive regulation of interleukin-1 alpha production / RAGE receptor binding / fibroblast growth factor binding / positive regulation of cytokine production / calcium-dependent protein binding / protein transport / regulation of cell shape / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / copper ion binding / lipid binding / positive regulation of cell population proliferation / calcium ion binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVaithiyalingam, S. / Kumar, T.K.S. / Yu, C.
CitationJournal: To be Published
Title: Three-Dimensional Solution Structure of S100A13
Authors: Vaithiyalingam, S. / Kumar, T.K.S. / Yu, C.
History
DepositionJun 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: S100 calcium-binding protein A13
B: S100 calcium-binding protein A13


Theoretical massNumber of molelcules
Total (without water)22,3502
Polymers22,3502
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein S100 calcium-binding protein A13 / S100A13


Mass: 11174.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pLys / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97352

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
1411H-15N HSQC
NMR detailsText: The structure was determined using standard 2D & 3D homo- and heteronuclear techniques

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Sample preparation

DetailsContents: Protein (S100A13) / Solvent system: 90% H20, D20
Sample conditionsIonic strength: 25mM Tris-HCl, 0.3mM Calcium / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS3.5Brukerprocessing
CNS1.1A.T. Brungerstructure solution
Sparky2T.L. Jamesdata analysis
CNS1.1A.T. Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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