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- PDB-2l50: Solution structure of apo S100A16 -

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Basic information

Entry
Database: PDB / ID: 2l50
TitleSolution structure of apo S100A16
ComponentsProtein S100-A16
KeywordsMETAL BINDING PROTEIN / apoS100A16 / EF-hand protein / S100 protein
Function / homology
Function and homology information


response to calcium ion / calcium-dependent protein binding / calcium ion binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / nucleus ...response to calcium ion / calcium-dependent protein binding / calcium ion binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...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 / Recoverin; domain 1 / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsBabini, E. / Bertini, I. / Borsi, V. / Calderone, V. / Hu, X. / Luchinat, C. / Parigi, G.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2011
Title: Structural characterization of human S100A16, a low-affinity calcium binder.
Authors: Babini, E. / Bertini, I. / Borsi, V. / Calderone, V. / Hu, X. / Luchinat, C. / Parigi, G.
History
DepositionOct 22, 2010Deposition site: BMRB / Processing site: RCSB
SupersessionNov 3, 2010ID: 2L0U
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-A16
B: Protein S100-A16


Theoretical massNumber of molelcules
Total (without water)23,3722
Polymers23,3722
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)30 / 350target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein S100-A16 / Aging-associated gene 13 protein / Protein S100-F / S100 calcium-binding protein A16


Mass: 11686.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A16, S100F, AAG13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FQ6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1823D HBHA(CO)NH
1913D (H)CCH-TOCSY
11023D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] APOS100A16, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 15N] APOS100A16, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMAPOS100A16-1[U-100% 13C; U-100% 15N]1
0.6 mMAPOS100A16-2[U-100% 15N]2
Sample conditionsIonic strength: 0.1 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmdata analysis
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
WHAT IFVriendstructure solution
WHAT IFVriendrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 350 / Conformers submitted total number: 30

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