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- PDB-2k7o: Ca2+-S100B, refined with RDCs -

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Basic information

Entry
Database: PDB / ID: 2k7o
TitleCa2+-S100B, refined with RDCs
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / S100 protein / calcium binding / EF-hand / Calcium / Cytoplasm / Metal-binding / Nucleus / Zinc
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 / response to methylmercury / ion binding ...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 / response to methylmercury / ion binding / 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 / simulated annealing
Model detailsSolution structure of Ca2+-S100B with two sets of RDC values included
AuthorsWright, N.T. / Inman, K.G. / Levine, J.A. / Weber, D.J.
CitationJournal: J.Biomol.Nmr / Year: 2008
Title: Refinement of the solution structure and dynamic properties of Ca(2+)-bound rat S100B.
Authors: Wright, N.T. / Inman, K.G. / Levine, J.A. / Cannon, B.R. / Varney, K.M. / Weber, D.J.
History
DepositionAug 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-B
B: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4146
Polymers21,2542
Non-polymers1604
Water0
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 lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein S100-B / S100 calcium-binding protein B / S-100 protein subunit beta / S-100 protein beta chain


Mass: 10626.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100b / Production host: Escherichia coli (E. coli) / 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
Details: Solution structure of Ca2+-S100B with two sets of RDC values included
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111IPAP
121HN(CO)CA

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Sample preparation

DetailsContents: 400 uM [U-15N] S100B, 10 mM CaCl2, 25 mM NaCl, 10 mM [U-99% 2H] MES, pH 6.7, 10 mM DTT, .1 mM NaN3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMS100B[U-15N]1
10 mMCaCl21
25 mMNaCl1
10 mMMES, pH 6.7[U-99% 2H]1
10 mMDTT1
0.1 mMNaN31
Sample conditionsIonic strength: 50 / pH: 6.7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloreprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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