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- PDB-1uwo: CALCIUM FORM OF HUMAN S100B, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1uwo
TitleCALCIUM FORM OF HUMAN S100B, NMR, 20 STRUCTURES
ComponentsS100B
KeywordsCALCIUM-BINDING PROTEIN / HUMAN S100B / EF-HAND / CONFORMATIONAL CHANGE / SOLUTION STRUCTURE
Function / homology
Function and homology information


adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / ion binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle ...adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / ion binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / axonogenesis / sarcoplasmic reticulum / central nervous system development / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / calcium-dependent protein binding / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / intracellular membrane-bounded organelle / 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 / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsSmith, S.P. / Shaw, G.S.
Citation
Journal: Structure / Year: 1998
Title: A novel calcium-sensitive switch revealed by the structure of human S100B in the calcium-bound form.
Authors: Smith, S.P. / Shaw, G.S.
#1: Journal: J.Biomol.NMR / Year: 1997
Title: Assignment and Secondary Structure of Calcium-Bound Human S100B
Authors: Smith, S.P. / Shaw, G.S.
History
DepositionDec 5, 1997Processing site: BNL
Revision 1.0Jun 10, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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)21,1922
Polymers21,1922
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 / 30LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein S100B / S-100B


Mass: 10595.841 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: NERVOUS / Cell: GLIAL / Cellular location: CYTOPLASM / Organ: BRAIN / Plasmid: PSS2 / Production host: Escherichia coli (E. coli) / Strain (production host): N99 / References: UniProt: P04271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCA(CO)NH
131HNCO
141HNHA
1511H-15N NOESY-HSQC
16115N/13C NOESY-HSQC
171NOESY

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Sample preparation

Sample conditionspH: 7.05 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY500 / Manufacturer: Varian / Model: UNITY500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES OF THE MONOMERS WERE CALCULATED USING MATRIX DISTANCE GEOMETRY, FOLLOWED BY SIMULATED ANNEALING. THE MONOMERS WERE THEN DUPLICATED AND EACH NEW SUBUNIT WAS ROTATED 180 DEGREES ...Details: THE STRUCTURES OF THE MONOMERS WERE CALCULATED USING MATRIX DISTANCE GEOMETRY, FOLLOWED BY SIMULATED ANNEALING. THE MONOMERS WERE THEN DUPLICATED AND EACH NEW SUBUNIT WAS ROTATED 180 DEGREES AND SEPARATELY FROM ITS PARTNER BY 40 ANGSTROMS. NO DOCKING OF THE TWO MONOMERS WAS ATTEMPTED PRIOR THE FURTHER STRUCTURE CALCULATIONS. DIMER STRUCTURE CALCULATIONS USED THE 40 UNAMBIGUOUS INTERMONOMER NOES TO BRING THE SUBUNITS IN A POSITION RELATIVE TO ONE ANOTHER. A FURTHER FOUR ROUNDS OF SIMULATED ANNEALING GENERATED THE FINAL STRUCTURES. AT NO POINT DURING THE DIMER CALCULATIONS WAS NON-CRYSTALLOGRAPHIC SYMMETRY UTILIZED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 30 / Conformers submitted total number: 20

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