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- PDB-3gin: Crystal structure of E454K-CBD1 -

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Basic information

Entry
Database: PDB / ID: 3gin
TitleCrystal structure of E454K-CBD1
ComponentsSodium/calcium exchanger 1
KeywordsMETAL BINDING PROTEIN / CBD1 / CBD2 / NCX / calcium binding domain 1 / Antiport / Calcium transport / Calmodulin-binding / Cell membrane / Glycoprotein / Ion transport / Membrane / Phosphoprotein / Sodium transport / Transmembrane / Transport / METAL TRANSPORT
Function / homology
Function and homology information


calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium:sodium antiporter activity / cell communication / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / calcium ion import / ankyrin binding / calcium ion import across plasma membrane / positive regulation of the force of heart contraction / sodium ion transmembrane transport ...calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium:sodium antiporter activity / cell communication / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / calcium ion import / ankyrin binding / calcium ion import across plasma membrane / positive regulation of the force of heart contraction / sodium ion transmembrane transport / positive regulation of bone mineralization / response to muscle stretch / calcium ion transmembrane transport / sarcolemma / postsynapse / calmodulin binding / axon / calcium ion binding / nucleoplasm / plasma membrane
Similarity search - Function
Sodium/calcium exchanger, isoform 1 / CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region ...Sodium/calcium exchanger, isoform 1 / CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / CalX-like domain superfamily / DnaJ domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChaptal, V. / Mercado-Besserer, G. / Abramson, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and functional analysis of a Ca2+ sensor mutant of the na+/ca2+ exchanger
Authors: Chaptal, V. / Ottolia, M. / Mercado-Besserer, G. / Nicoll, D.A. / Philipson, K.D. / Abramson, J.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/calcium exchanger 1
B: Sodium/calcium exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2059
Polymers34,9242
Non-polymers2817
Water1,76598
1
A: Sodium/calcium exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6225
Polymers17,4621
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sodium/calcium exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5824
Polymers17,4621
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.858, 91.858, 65.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 17462.182 Da / Num. of mol.: 2 / Fragment: Calx-beta 1 domain / Mutation: E454K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SLC8A1 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P23685
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: mother liquor: 3.5 M ammonium chloride, 0.1 M sodium acetate, protein concentration: 20 mg/ml, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→65 Å / Num. all: 11458 / Num. obs: 10733 / % possible obs: 98.34 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.4→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DPK

2dpk


Resolution: 2.4→64.96 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.067 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.366 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25862 535 4.7 %RANDOM
Rwork0.19298 ---
obs0.19615 10733 98.34 %-
all-11458 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→64.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 7 98 1896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221815
X-RAY DIFFRACTIONr_bond_other_d0.0010.021180
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.942457
X-RAY DIFFRACTIONr_angle_other_deg0.8932881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48525.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.862158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_nbd_refined0.230.2287
X-RAY DIFFRACTIONr_nbd_other0.1980.21188
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2838
X-RAY DIFFRACTIONr_nbtor_other0.0860.21073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.284
X-RAY DIFFRACTIONr_metal_ion_refined0.190.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.29
X-RAY DIFFRACTIONr_mcbond_it0.7621.51176
X-RAY DIFFRACTIONr_mcbond_other0.1441.5481
X-RAY DIFFRACTIONr_mcangle_it1.33821852
X-RAY DIFFRACTIONr_scbond_it2.023707
X-RAY DIFFRACTIONr_scangle_it3.1214.5605
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 34 -
Rwork0.268 765 -
obs--97.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8489-2.73950.87172.8151-0.26491.0114-0.0120.07580.0860.0179-0.038-0.0534-0.03650.10070.05-0.0742-0.01810.017-0.07490.0093-0.0853-17.3311-9.611-16.5326
24.6526-2.27530.7273.13810.25842.1170.11150.1393-0.0718-0.043-0.0053-0.04790.21710.0678-0.1061-0.068-0.0107-0.0038-0.1034-0.0102-0.1144-29.9389-25.646-15.5972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A370 - 501
2X-RAY DIFFRACTION2B370 - 501

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