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- PDB-4kjs: Structure of native YfkE -

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Basic information

Entry
Database: PDB / ID: 4kjs
TitleStructure of native YfkE
Componentscation exchanger YfkE
KeywordsTRANSPORT PROTEIN / YfkE / CaCA / Ca/H+ antiporter / CAX
Function / homology
Function and homology information


calcium:proton antiporter activity / calcium ion transmembrane transport / intracellular calcium ion homeostasis / plasma membrane
Similarity search - Function
Calcium/proton exchanger / Calcium/proton exchanger CAX-like / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein
Similarity search - Domain/homology
Ca(2+)/H(+) antiporter ChaA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsWu, M. / Tong, S. / Zheng, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation.
Authors: Wu, M. / Tong, S. / Waltersperger, S. / Diederichs, K. / Wang, M. / Zheng, L.
History
DepositionMay 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: cation exchanger YfkE
B: cation exchanger YfkE


Theoretical massNumber of molelcules
Total (without water)75,0042
Polymers75,0042
Non-polymers00
Water32418
1
A: cation exchanger YfkE

A: cation exchanger YfkE

A: cation exchanger YfkE


Theoretical massNumber of molelcules
Total (without water)112,5073
Polymers112,5073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6920 Å2
ΔGint-78 kcal/mol
Surface area37210 Å2
MethodPISA
2
B: cation exchanger YfkE

B: cation exchanger YfkE

B: cation exchanger YfkE


Theoretical massNumber of molelcules
Total (without water)112,5073
Polymers112,5073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6920 Å2
ΔGint-80 kcal/mol
Surface area36400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.505, 168.505, 94.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein cation exchanger YfkE


Mass: 37502.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: yfkE, BSU07920 / Production host: Escherichia coli (E. coli) / References: UniProt: O34840
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 23-25% PEG400, 0.2M Ammonium Sulfate, 20mM NaCl, 0.1M NaAc pH4.0, 3% Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.6 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.486
11K, H, -L20.514
ReflectionResolution: 2.9→84 Å / Num. all: 22199 / Num. obs: 21979 / % possible obs: 99.9 % / Observed criterion σ(I): 17.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→50.01 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26187 945 5 %RANDOM
Rwork0.21623 ---
obs0.21856 18024 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.565 Å2
Baniso -1Baniso -2Baniso -3
1-9.63 Å20 Å20 Å2
2--9.63 Å20 Å2
3----19.25 Å2
Refinement stepCycle: LAST / Resolution: 3.05→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 0 18 4800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.966634
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02223.6150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.40215786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.052158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023460
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.048→3.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 50 -
Rwork0.209 1327 -
obs--97.59 %

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