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- PDB-2jnx: NMR derived solution structure of an EF-hand Calcium Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 2jnx
TitleNMR derived solution structure of an EF-hand Calcium Binding Protein from Entamoeba Histolytica
ComponentsCalcium binding protein 2
KeywordsMETAL BINDING PROTEIN / Calcium Binding Protein / EhCaBP2
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Recoverin family / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / 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. ...Recoverin family / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / 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 2
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsNMR Derived Solution Structure of an EF-hand Calcium Binding Protein from Entamoeba Histolytica
AuthorsMustafi, S.M. / Mutalik, R.B. / Chary, K.V.
CitationJournal: To be Published
Title: Structure, dynamics, and physiological properties of a Calcium Binding Protein from Entamoeba Histolytica (EhCaBP2)
Authors: Mustafi, S.M. / Mutalik, R.B.
History
DepositionFeb 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1215
Polymers14,9611
Non-polymers1604
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 / 400target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Calcium binding protein 2


Mass: 14960.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6R3G0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR Derived Solution Structure of an EF-hand Calcium Binding Protein from Entamoeba Histolytica
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1223D 1H-15N NOESY
1323D 1H-15N TOCSY
1422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 13C; U-100% 15N] protein, 150 mM Sodium acetate-acetic acid buffer, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-100% 15N] protein, 100 mM NaCl, 20 mM CaCl2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMammonium acetate[U-100% 13C; U-100% 15N]1
1 mMammonium acetate[U-100% 15N]2
Sample conditionspH: 4.2 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Braun and Wuthrichstructure solution
DYANA1.5Guntert, Braun and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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