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- PDB-1jfj: NMR SOLUTION STRUCTURE OF AN EF-HAND CALCIUM BINDING PROTEIN FROM... -

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Basic information

Entry
Database: PDB / ID: 1jfj
TitleNMR SOLUTION STRUCTURE OF AN EF-HAND CALCIUM BINDING PROTEIN FROM ENTAMOEBA HISTOLYTICA
ComponentsCALCIUM-BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / EF-HAND / HELIX-LOOP-HELIX / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of macropinocytosis / regulation of actin filament bundle assembly / regulation of protein kinase activity / phagocytic cup / pseudopodium / actin monomer binding / positive regulation of phagocytosis / phagocytosis / actin filament binding / calcium ion binding / cytoplasm
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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
Calcium-binding protein 1
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAtreya, H.S. / Sahu, S.C. / Bhattacharya, A. / Chary, K.V.R. / Govil, G.
CitationJournal: Biochemistry / Year: 2001
Title: NMR derived solution structure of an EF-hand calcium-binding protein from Entamoeba Histolytica.
Authors: Atreya, H.S. / Sahu, S.C. / Bhattacharya, A. / Chary, K.V. / Govil, G.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,9711
Polymers14,9711
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein CALCIUM-BINDING PROTEIN / / EHCABP


Mass: 14970.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Plasmid: PET-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38505

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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
1322D NOESY
1423D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM EHCaBP, 30mM Deuterated Tris buffer, 30mM Calc290% H2O/10% D2O
23mM EHCaBP, 30mM Deuterated Tris buffer, 30mM Cacl2100% D2O
Sample conditionsIonic strength: 10mM Cacl2 / pH: 6.0 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, Mumenthaler and Wuthrichstructure solution
DYANA1.5Guentert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structure is based on a total of 1265 NOE-derived distance constraints, 200 dihedral angle constraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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