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- PDB-1xyd: NMR Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures -

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Basic information

Entry
Database: PDB / ID: 1xyd
TitleNMR Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures
ComponentsS-100 protein, beta chain
KeywordsMETAL BINDING PROTEIN
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 / distance geometry, simulated annealing
AuthorsWilder, P.T. / Varney, K.M. / Weber, D.J.
CitationJournal: Biochemistry / Year: 2005
Title: Solution Structure of Zinc- and Calcium-Bound Rat S100B as Determined by Nuclear Magnetic Resonance Spectroscopy
Authors: Wilder, P.T. / Varney, K.M. / Weiss, M.B. / Gitti, R.K. / Weber, D.J.
History
DepositionNov 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-100 protein, beta chain
B: S-100 protein, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8078
Polymers21,5162
Non-polymers2916
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
Representative

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Components

#1: Protein S-100 protein, beta chain / S100B


Mass: 10758.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100b / 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111Fast HSQC
1213D 15N-separated NOESY
1313D 15N-edited HOHAHA-HSQC
1413D 15N,15N-edited HMQC-NOESY-HSQC
151HNHA
1623D CBCA(CO)NH
173Long range HSQC
1823D HNCA, 3D HNCO, and 3D HN(CA)CB
1924D 13C-separated NOESY
11024D 13C/15N-separated NOESY

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Sample preparation

Details
Solution-IDContents
13 mM 15N S100B (monomer concentration), 3 mM Zinc acetate, 10 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O
23 mM 15N,13C S100B (monomer concentration), 3 mM Zinc acetate, 10 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O
31 mM 15N S100B (monomer concentration), 1 mM Zinc acetate, 3.3 mM CaCl2, 0.34 mM NaN3, 15 mM NaCl, <0.07 mM DTT, 10 mM TES, 10% D2O
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 310.15 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionClassification
NMRPipeprocessing
X-PLORxplor-nih-2.9.2refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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