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- PDB-1qlk: SOLUTION STRUCTURE OF CA(2+)-LOADED RAT S100B (BETABETA) NMR, 20 ... -

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Entry
Database: PDB / ID: 1qlk
TitleSOLUTION STRUCTURE OF CA(2+)-LOADED RAT S100B (BETABETA) NMR, 20 STRUCTURES
ComponentsS-100 PROTEIN
KeywordsCALCIUM-BINDING / S100BETA / S100B / EF-HAND / S100 PROTEIN / CALCIUM-BINDING PROTEIN / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


negative regulation of skeletal muscle cell differentiation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / sympathetic neuron projection extension / positive regulation of myelination / RAGE receptor binding / ion binding / response to methylmercury ...negative regulation of skeletal muscle cell differentiation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / sympathetic neuron projection extension / positive regulation of myelination / RAGE receptor binding / ion 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 / sarcoplasmic reticulum / 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
AuthorsDrohat, A.C. / Baldisseri, D.M. / Rustandi, R.R. / Weber, D.J.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structure of calcium-bound rat S100B(betabeta) as determined by nuclear magnetic resonance spectroscopy,.
Authors: Drohat, A.C. / Baldisseri, D.M. / Rustandi, R.R. / 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. / Weber, D.J.
#2: Journal: J.Biomol.NMR / Year: 1995
Title: 1H, 13C and 15N NMR Assignments and Solution Secondary Structure of Rat Apo-S100 Beta
Authors: Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Shah, S. / Hilt, D.C. / Weber, D.J.
History
DepositionSep 26, 1997Processing site: BNL
Revision 1.0Nov 11, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: S-100 PROTEIN
B: S-100 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6766
Polymers21,5162
Non-polymers1604
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 / 20SEE MAIN REFERENCE
RepresentativeModel #1

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Components

#1: Protein S-100 PROTEIN


Mass: 10758.048 Da / Num. of mol.: 2 / Fragment: SUBUNITS A AND B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100BETA / Plasmid: PET11B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: P04631
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE MAIN REFERENCE
NMR detailsText: PLEASE SEE MAIN REFERENCE FOR DETAILS

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Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: 22mM / pH: 6.5 / Pressure: ATMOSPHERIC 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

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR V3.851(ONLINE)V3.851(ONLINE)structure solution
RefinementMethod: SEE MAIN REFERENCE / Software ordinal: 1
NMR ensembleConformer selection criteria: SEE MAIN REFERENCE / Conformers calculated total number: 20 / Conformers submitted total number: 20

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