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- PDB-1zfs: Solution structure of S100A1 bound to calcium -

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Basic information

Entry
Database: PDB / ID: 1zfs
TitleSolution structure of S100A1 bound to calcium
ComponentsS-100 protein, alpha chain
KeywordsMETAL BINDING PROTEIN / S100 / noncovalent homodimer / x-type 4 helix bundle / calcium binding / conformational change
Function / homology
Function and homology information


Regulation of TLR by endogenous ligand / RAGE receptor binding / M band / I band / S100 protein binding / A band / regulation of heart contraction / positive regulation of sprouting angiogenesis / sarcoplasmic reticulum / Z disc ...Regulation of TLR by endogenous ligand / RAGE receptor binding / M band / I band / S100 protein binding / A band / regulation of heart contraction / positive regulation of sprouting angiogenesis / sarcoplasmic reticulum / Z disc / calcium-dependent protein binding / ATPase binding / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / extracellular space / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein S100-A1 / 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-A1 / 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 (DGSA)
AuthorsWright, N.T. / Varney, K.M. / Weber, D.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The three-dimensional solution structure of Ca(2+)-bound S100A1 as determined by NMR spectroscopy
Authors: Wright, N.T. / Varney, K.M. / Ellis, K.C. / Markowitz, J. / Gitti, R.K. / Zimmer, D.B. / Weber, D.J.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,0406
Polymers20,8792
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)19 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein S-100 protein, alpha chain


Mass: 10439.614 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100a1 / Plasmid: pET11B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 / References: UniProt: P35467
#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 experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-separated NOESY
1214D 13C/15N-separated NOESY
1313D 15N-separated NOESY
141HNHA
NMR detailsText: RDC data using radially and axially compressed acrylamide gels were added into structure calculations. H-bonds were determined using hydrogen exchange experiments

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Sample preparation

DetailsContents: 0.5-3 mM S100A1 monomer, U-15N, 13C, 0.35 mM NaN3, 15 mM NaCl, 20 mM CaCl2, 25 mM Tris, 25 mM DTT, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 15 mM / pH: 7.2 / Pressure: ambient / Temperature: 310 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
NameVersionDeveloperClassification
X-PLOR2.9.3C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorestructure solution
X-PLOR2.9.3C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorerefinement
RefinementMethod: distance geometry simulated annealing (DGSA) / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 19

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