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- PDB-2luc: Solution Structure of human S100 calcium-binding protein A11 -

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Basic information

Entry
Database: PDB / ID: 2luc
TitleSolution Structure of human S100 calcium-binding protein A11
ComponentsProtein S100-A11
KeywordsMETAL BINDING PROTEIN / EF-hand motif / homodimer / calcium-binding protein
Function / homology
Function and homology information


cadherin binding involved in cell-cell adhesion / S100 protein binding / negative regulation of DNA replication / positive regulation of smooth muscle cell migration / ruffle / adherens junction / calcium-dependent protein binding / secretory granule lumen / negative regulation of cell population proliferation / calcium ion binding ...cadherin binding involved in cell-cell adhesion / S100 protein binding / negative regulation of DNA replication / positive regulation of smooth muscle cell migration / ruffle / adherens junction / calcium-dependent protein binding / secretory granule lumen / negative regulation of cell population proliferation / calcium ion binding / Neutrophil degranulation / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm
Similarity search - Function
Protein S100-A11 / 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-A11 / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHung, K.W. / Chang, Y.M. / Yu, C.
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: NMR structure note: the structure of human calcium-bound S100A11.
Authors: Hung, K.W. / Chang, Y.M. / Yu, C.
History
DepositionJun 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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-A11
B: Protein S100-A11


Theoretical massNumber of molelcules
Total (without water)23,5092
Polymers23,5092
Non-polymers00
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 #1lowest energy

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Components

#1: Protein Protein S100-A11 / Calgizzarin / Metastatic lymph node gene 70 protein / MLN 70 / Protein S100-C / S100 calcium- ...Calgizzarin / Metastatic lymph node gene 70 protein / MLN 70 / Protein S100-C / S100 calcium-binding protein A11


Mass: 11754.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A11, MLN70, S100C / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P31949

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HNCO
1813D HN(CA)CO
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D 15N-edited NOESY-HSQC
11213D 13C-edited NOESY-HSQC
11313D 13C F1-filtered, F3-edited NOESY-HSQC
11413D HBHA(CO)NH
11513D H(CCO)NH
11613D C(CO)NH

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] S100A11, 25 mM TRIS, 100 mM sodium chloride, 5 mM calcium chloride, 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMS100A11-1[U-100% 13C; U-100% 15N]1
25 mMTRIS-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
90 %H2O-51
10 %D2O-61
Sample conditionsIonic strength: 0.0725 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
VnmrJVarianprocessing
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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