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- PDB-1b4c: SOLUTION STRUCTURE OF RAT APO-S100B USING DIPOLAR COUPLINGS -

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Basic information

Entry
Database: PDB / ID: 1b4c
TitleSOLUTION STRUCTURE OF RAT APO-S100B USING DIPOLAR COUPLINGS
ComponentsPROTEIN (S-100 PROTEIN, BETA CHAIN)
KeywordsMETAL BINDING PROTEIN / S100BETA / S100B / DIPOLAR COUPLINGS / EF-HAND / S100 PROTEIN / CALCIUM- BINDING PROTEIN / FOUR-HELIX BUNDLE / THREE-DIMENSIONAL STRUCTURE / SOLUTION STRUCTURE
Function / homology
Function and homology information


negative regulation of skeletal muscle cell differentiation / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / adaptive thermogenesis / sympathetic neuron projection extension / positive regulation of myelination / RAGE receptor binding / response to methylmercury / astrocyte differentiation ...negative regulation of skeletal muscle cell differentiation / TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / adaptive thermogenesis / sympathetic neuron projection extension / positive regulation of myelination / RAGE receptor binding / response to methylmercury / astrocyte differentiation / S100 protein binding / neuron projection extension / regulation of neuronal synaptic plasticity / positive regulation of synaptic transmission / response to glucocorticoid / ruffle / positive regulation of neuron differentiation / long-term synaptic potentiation / tau protein binding / memory / calcium-dependent protein binding / regulation of cell shape / cellular response to hypoxia / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / positive regulation of apoptotic process / signaling receptor binding / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein S100-B / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-B / 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 / Recoverin; domain 1 / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / SEE MAIN REFERENCE
AuthorsWeber, D.J. / Drohat, A.C. / Tjandra, N. / Baldisseri, D.M.
Citation
Journal: Protein Sci. / Year: 1999
Title: The use of dipolar couplings for determining the solution structure of rat apo-S100B(betabeta).
Authors: Drohat, A.C. / Tjandra, N. / Baldisseri, D.M. / Weber, D.J.
#1: Journal: Biochemistry / Year: 1996
Title: Solution Structure of Rat Apo-S100B(beta beta) as Determined by NMR Spectroscopy
Authors: Drohat, A.C. / Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Baldisseri, D.M. / Weber, D.J.
#2: Journal: J.Biomol.NMR / Year: 1995
Title: ==1==H, ==13==C and ==15==N NMR Assignments and Solution Secondary Structure of Rat Apo-S100Beta
Authors: Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Shah, S. / Hilt, D.C. / Weber, D.J.
History
DepositionDec 17, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units
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: PROTEIN (S-100 PROTEIN, BETA CHAIN)
B: PROTEIN (S-100 PROTEIN, BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)21,5162
Polymers21,5162
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)21 / 21SEE MAIN REFERENCE
RepresentativeModel #2

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Components

#1: Protein PROTEIN (S-100 PROTEIN, BETA CHAIN) / S100B / S100BETA


Mass: 10758.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: S100B IS A HOMODIMER OF S100BETA SUBUNITS / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: SEE MAIN REFERENCE / Gene: S100BETA FROM RATTUS NORVEGICUS (RAT) / Plasmid: PET11B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P04631

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE MAIN REFERENCE
NMR detailsText: SEE MAIN REFERENCE

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Sample preparation

Sample conditionsIonic strength: 25mM / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600.13 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR V3.851V3.851AXEL T. BRUNGERrefinement
X-PLOR V3.851V3.851structure solution
RefinementMethod: SEE MAIN REFERENCE / Software ordinal: 1 / Details: SEE MAIN REFERENCE
NMR ensembleConformer selection criteria: SEE MAIN REFERENCE / Conformers calculated total number: 21 / Conformers submitted total number: 21

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