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- PDB-5hxr: Structural mechanisms of extracellular ion exchange and induced b... -

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Basic information

Entry
Database: PDB / ID: 5hxr
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 10mM Ca2+
Componentssodium,calcium exchanger
KeywordsMEMBRANE PROTEIN / Na+/Ca2+ exchange / Calcium signalling / membrane transporter / induced conformational change
Function / homology
Function and homology information


calcium, potassium:sodium antiporter activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / plasma membrane
Similarity search - Function
NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / A middle domain of Talin 1 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special ...NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / A middle domain of Talin 1 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PENTADECANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / Uncharacterized membrane protein MJ0091
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.463 Å
AuthorsLiao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D.
Funding support China, United States, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaProject 31470817 China
Howard Hughes Medical Institutefor Youxing Jiang United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079179 United States
Welch FoundationGrant I-1578 United States
National Institutes of HealthDivision of Intramural Research of National Heart, Lung and Blood Institute United States
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger
Authors: Liao, J. / Marinelli, F. / Lee, C. / Huang, Y. / Faraldo-Gomez, J.D. / Jiang, Y.
#1: Journal: Science / Year: 2012
Title: Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger
Authors: Liao, J. / Li, H. / Zeng, W. / Sauer, D.B. / Belmares, R. / Jiang, Y.
History
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: entity / pdbx_audit_support ...entity / pdbx_audit_support / pdbx_struct_oper_list / struct
Item: _entity.pdbx_description / _pdbx_audit_support.funding_organization ..._entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct.pdbx_descriptor
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 8, 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

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Assembly

Deposited unit
A: sodium,calcium exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,88415
Polymers32,0291
Non-polymers2,85514
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 72.522, 96.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein sodium,calcium exchanger


Mass: 32029.131 Da / Num. of mol.: 1 / Fragment: UNP residues 1-300 / Mutation: L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57556

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Non-polymers , 5 types, 30 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H32
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / Details: PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 13042 / % possible obs: 99.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 59.14 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.055 / Rrim(I) all: 0.126 / Χ2: 1.517 / Net I/av σ(I): 24.354 / Net I/σ(I): 6.9 / Num. measured all: 101923
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.45-2.497.86360.6110.781.074100
2.49-2.547.96290.670.6381.106100
2.54-2.597.96550.7260.5231.142100
2.59-2.647.96270.8050.4651.226100
2.64-2.77.86350.8180.4141.423100
2.7-2.7686440.8750.3871.242100
2.76-2.8386420.9170.321.3081000.8750.933
2.83-2.986510.9260.2641.2861000.7160.764
2.9-2.998.16410.9560.2041.3711000.5580.595
2.99-3.0986440.9510.1831.4011000.4990.533
3.09-3.28.16400.9680.1611.4921000.440.469
3.2-3.328.16530.9790.1211.4941000.330.352
3.32-3.4886530.9860.1081.8931000.2930.312
3.48-3.6686550.9930.0691.98699.80.1860.198
3.66-3.897.96450.9920.0581.9791000.1560.166
3.89-4.197.96730.9960.0411.951000.1090.116
4.19-4.616.66260.9960.0331.80195.10.0810.088
4.61-5.287.86740.9980.0261.8241000.070.075
5.28-6.657.86830.9980.0261.5351000.070.075
6.65-5077360.9980.0211.80498.40.0510.056

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V5U

3v5u


Resolution: 2.463→31.302 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1040 8 %
Rwork0.2213 11956 -
obs0.2244 12996 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.49 Å2 / Biso mean: 65.5915 Å2 / Biso min: 36.59 Å2
Refinement stepCycle: final / Resolution: 2.463→31.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 117 16 2331
Biso mean--78.68 69.36 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022356
X-RAY DIFFRACTIONf_angle_d0.633162
X-RAY DIFFRACTIONf_chiral_restr0.022386
X-RAY DIFFRACTIONf_plane_restr0.004371
X-RAY DIFFRACTIONf_dihedral_angle_d9.476855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4634-2.59320.30271340.25471549168391
2.5932-2.75560.27131470.241516921839100
2.7556-2.96820.29221480.235817001848100
2.9682-3.26660.25481520.221217321884100
3.2666-3.73860.25831490.225917231872100
3.7386-4.70770.28841490.21021714186398
4.7077-31.30430.23111610.218418462007100

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