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- PDB-2kls: Apo-form of the second Ca2+ binding domain of NCX1.4 -

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Basic information

Entry
Database: PDB / ID: 2kls
TitleApo-form of the second Ca2+ binding domain of NCX1.4
ComponentsSodium/calcium exchanger 1
KeywordsMETAL BINDING PROTEIN / sodium calcium exchanger / electrostatic switch / Ca2+ sensor / Ca2+ regulation
Function / homologyCalX-beta domain / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCanis familiaris (dog)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 5
AuthorsHilge, M. / Aelen, J. / Foarce, A. / Perrakis, A. / Vuister, G.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Ca2+ regulation in the Na+/Ca2+ exchanger features a dual electrostatic switch mechanism.
Authors: Hilge, M. / Aelen, J. / Foarce, A. / Perrakis, A. / Vuister, G.W.
History
DepositionJul 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/calcium exchanger 1


Theoretical massNumber of molelcules
Total (without water)18,7281
Polymers18,7281
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sodium/calcium exchanger 1 / Na(+)/Ca(2+)-exchange protein 1


Mass: 18727.838 Da / Num. of mol.: 1 / Fragment: Second Ca2+ binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis familiaris (dog) / Gene: SLC8A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / Variant (production host): DE3
Sequence detailsTHE DIFFERENCES BETWEEN THE DEPOSITED SEQUENCE AND THE SEQUENCE OF UNP ENTRY P23685 ORIGINATE FROM ...THE DIFFERENCES BETWEEN THE DEPOSITED SEQUENCE AND THE SEQUENCE OF UNP ENTRY P23685 ORIGINATE FROM THE FACT THAT THERE ARE SEVERAL SPLICE FORMS. P23685 CONTAINS ALL EXONS (A,C,D,E AND F). THE DEPOSITED STRUCTURE CONTAINS ONLY EXONS A AND D (OFTEN ALSO TERMED AS NCX1.4).

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D (H)CCH-TOCSY
1513D HNHA
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] Na+/Ca2+ exchanger, 20 mM Hepes, 20 mM b-mercaptoethanol, 10mM EDTA, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNa+/Ca2+ exchanger-1[U-100% 13C; U-100% 15N]1
20 mMHepes-21
20 mMb-mercaptoethanol-31
10 mMEDTA-41
Sample conditionsIonic strength: 0.02 / pH: 7.0 / Pressure: ambient / Temperature: 306 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Herrmann, Guntert, Wuthrichstructure solution
X-PLORBrungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2623 / NOE long range total count: 1288
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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