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- PDB-2m0r: Solution structure and dynamics of human S100A14 -

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Basic information

Entry
Database: PDB / ID: 2m0r
TitleSolution structure and dynamics of human S100A14
ComponentsProtein S100-A14
KeywordsMETAL BINDING PROTEIN / EF-hand proteins / Protein dynamics
Function / homology
Function and homology information


positive regulation of granulocyte chemotaxis / chemokine receptor binding / positive regulation of monocyte chemotaxis / toll-like receptor 4 signaling pathway / calcium ion homeostasis / calcium-dependent protein binding / response to lipopolysaccharide / defense response to bacterium / apoptotic process / calcium ion binding ...positive regulation of granulocyte chemotaxis / chemokine receptor binding / positive regulation of monocyte chemotaxis / toll-like receptor 4 signaling pathway / calcium ion homeostasis / calcium-dependent protein binding / response to lipopolysaccharide / defense response to bacterium / apoptotic process / calcium ion binding / perinuclear region of cytoplasm / extracellular space / extracellular exosome
Similarity search - Function
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 domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsclosest to the average, model 23
AuthorsBertini, I. / Borsi, V. / Cerofolini, L. / Das Gupta, S. / Fragai, M. / Luchinat, C.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2013
Title: Solution structure and dynamics of human S100A14.
Authors: Bertini, I. / Borsi, V. / Cerofolini, L. / Das Gupta, S. / Fragai, M. / Luchinat, C.
History
DepositionNov 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jun 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 1.3May 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-A14
B: Protein S100-A14


Theoretical massNumber of molelcules
Total (without water)23,3542
Polymers23,3542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1962.23 Å2
ΔGint-14.9739 kcal/mol
Surface area8442.03 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 500target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein S100-A14 / S100 calcium-binding protein A14 / S114


Mass: 11677.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A14, S100A15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HCY8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HN(CA)CO
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11112D CON
11212D CACO
11312D CBCACO
11412D 1H-1H NOESY

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Sample preparation

DetailsContents: 100 mM sodium chloride, 5 mM DTT, 30 mM MES, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium chloride-11
5 mMDTT-21
30 mMMES-31
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
CARA2(CARA) Keller, R.L.J.chemical shift assignment
CING(CING) Vuister, G.W.structure validation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 30

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