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- PDB-1k2h: Three-dimensional Solution Structure of apo-S100A1. -

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Basic information

Entry
Database: PDB / ID: 1k2h
TitleThree-dimensional Solution Structure of apo-S100A1.
ComponentsS-100 protein, alpha chain
KeywordsMETAL BINDING PROTEIN / Non-covalent homodimer / X-type four-helix bundle
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, docking, molecular dynamics
AuthorsRustandi, R.R. / Baldisseri, D.M. / Inman, K.G. / Nizner, P. / Hamilton, S.M. / Landar, A. / Landar, A. / Zimmer, D.B. / Weber, D.J.
CitationJournal: Biochemistry / Year: 2002
Title: Three-dimensional solution structure of the calcium-signaling protein apo-S100A1 as determined by NMR.
Authors: Rustandi, R.R. / Baldisseri, D.M. / Inman, K.G. / Nizner, P. / Hamilton, S.M. / Landar, A. / Landar, A. / Zimmer, D.B. / Weber, D.J.
History
DepositionSep 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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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


Theoretical massNumber of molelcules
Total (without water)20,8792
Polymers20,8792
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 / 75structures with the least restraint violations
RepresentativeModel #17lowest energy

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Components

#1: Protein S-100 protein, alpha chain / S100A1


Mass: 10439.614 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET-11b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P35467

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1312D 1H-15N HSQC
1413D 15N separated HOHAHA
1524D 13C-separated NOESY
1623D HN(CA)CB
NMR detailsText: This structure was determined using constraints generated from heteronuclear, multi-dimensional NMR experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
1SAMPLE 1: S100A1, U-15N; 12-15mM d11-tris, 1-2mM EGTA, 0.3mM NaN3, 15-18mM NaCl; pH 6.4, 95% H2O, 5% D2O. SAMPLE 2: S100A1, U-13C,15N; 12-15mM d11-tris, 1-2mM EGTA, 0.3mM NaN3, 15-18mM NaCl; pH 6.4, 95% H2O, 5% D2O.95% H2O/5% D2O
2S100A1, U-13C,15N; 12-15mM d11-tris, 1-2mM EGTA, 0.3mM NaN3, 15-18mM NaCl; pH 6.4, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 25mM / pH: 6.4 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Analytik GmbHcollection
NMRPipe1.8F. Delaglioprocessing
X-PLOR3.851A. Brungerstructure solution
CHARMMHarvard Universitystructure solution
CHARMMHarvard Universityrefinement
RefinementMethod: distance geometry, simulated annealing, docking, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 75 / Conformers submitted total number: 20

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