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- PDB-1cfp: S100B (S100BETA) NMR DATA WAS COLLECTED FROM A SAMPLE OF CALCIUM ... -

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Basic information

Entry
Database: PDB / ID: 1cfp
TitleS100B (S100BETA) NMR DATA WAS COLLECTED FROM A SAMPLE OF CALCIUM FREE PROTEIN AT PH 6.3 AND A TEMPERATURE OF 311 K AND 1.7-6.9 MM CONCENTRATION, 25 STRUCTURES
ComponentsS100B
KeywordsCALCIUM-BINDING PROTEIN / HELIX-LOOP-HELIX
Function / homology
Function and homology information


Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding ...Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding / axonogenesis / sarcoplasmic reticulum / astrocyte activation / tau protein binding / calcium-dependent protein binding / regulation of translation / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / phosphorylation / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / 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 speciesBos taurus (cattle)
MethodSOLUTION NMR / DISTANCE GEOMETRY-SIMULATED ANNEALING
AuthorsKilby, P.M. / Vaneldik, L.J. / Roberts, G.C.K.
CitationJournal: Structure / Year: 1996
Title: The solution structure of the bovine S100B protein dimer in the calcium-free state.
Authors: Kilby, P.M. / Van Eldik, L.J. / Roberts, G.C.
History
DepositionJun 4, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: S100B
B: S100B


Theoretical massNumber of molelcules
Total (without water)21,3642
Polymers21,3642
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 / 91TOTAL ENERGY
Representative

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Components

#1: Protein S100B / S100BETA / S-100B


Mass: 10681.974 Da / Num. of mol.: 2
Mutation: N-TERMINAL METHIONINE REPLACES N-TERMINAL ACETYL GROUP OF THE NATURAL PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle)
Description: THE GENE IS A SYNTHETIC DNA FOR THE BOVINE SEQUENCE WITH ESCHERICHIA COLI CODON USAGE
Gene: S100B / Plasmid: PET-12A-S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P02638

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D NOESY-HMQC
1213D TOCSY-HMQC
1313D HMQC-NOESY-HMQC
1412D DOUBLE QUANTUM FILTERED COSY
NMR detailsText: S100B (S100BETA) NMR DATA WAS COLLECTED FROM A OF CALCIUM FREE PROTEIN AT PH 6.3 AND A TEMPERATURE OF 311 K AND 1.7-6.9 MM CONCENTRATION IONIC_STRENGTH : 20 MM SODIUM SUCCINATE PRESSURE : ...Text: S100B (S100BETA) NMR DATA WAS COLLECTED FROM A OF CALCIUM FREE PROTEIN AT PH 6.3 AND A TEMPERATURE OF 311 K AND 1.7-6.9 MM CONCENTRATION IONIC_STRENGTH : 20 MM SODIUM SUCCINATE PRESSURE : ATMOSPHERIC SOLVENT SYSTEM : 90% H2O : 10% D2O SOFTWARE PROGRAM(S) USED TO DETERMINE THE STRUCTURE : X-PLOR 3.841 METHOD USED TO DETERMINE THE STRUCTURE : DISTANCE GEOMETRY-SIMULATED ANNEALING

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 314 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX 600BrukerAMX 6005001
Bruker DMX 500BrukerDMX 5006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.841BRUNGERrefinement
X-PLOR3.841structure solution
RefinementMethod: DISTANCE GEOMETRY-SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 91 / Conformers submitted total number: 25

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