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- PDB-8poo: Low resolution structure of inactive conformation of the Ktr cati... -

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Basic information

Entry
Database: PDB / ID: 8poo
TitleLow resolution structure of inactive conformation of the Ktr cation channel in presence of ATP and c-di-AMP
Components
  • Ktr system potassium uptake protein A
  • Ktr system potassium uptake protein B
KeywordsMEMBRANE PROTEIN / Ktr channel
Function / homology
Function and homology information


potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Ktr system potassium uptake protein A / Ktr system potassium uptake protein B
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.77 Å
AuthorsCereija, T.B. / Teixeira-Duarte, C.M. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: c-di-AMP determines the hierarchical organization of bacterial RCK proteins.
Authors: Rocha, R. / Jorge, J.M.P. / Teixeira-Duarte, C.M. / Figueiredo-Costa, I.R. / Cereija, T.B. / Ferreira-Teixeira, P.F. / Herzberg, C. / Stulke, J. / Morais-Cabral, J.H.
History
DepositionJul 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B
A: Ktr system potassium uptake protein B
B: Ktr system potassium uptake protein B
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A


Theoretical massNumber of molelcules
Total (without water)322,0418
Polymers322,0418
Non-polymers00
Water0
1
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B

C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A


Theoretical massNumber of molelcules
Total (without water)225,0986
Polymers225,0986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
2
A: Ktr system potassium uptake protein B
B: Ktr system potassium uptake protein B
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A


Theoretical massNumber of molelcules
Total (without water)225,0986
Polymers225,0986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.795, 143.686, 160.669
Angle α, β, γ (deg.)90.000, 112.372, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Ktr system potassium uptake protein B / K(+)-uptake protein KtrB


Mass: 48471.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ktrB, yubG, BSU31100 / Production host: Escherichia coli (E. coli) / References: UniProt: O32081
#2: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 32038.717 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080

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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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl pH 8.5 700 mM KCl 24% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 5.77→49.53 Å / Num. obs: 15151 / % possible obs: 98.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 367.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Rsym value: 0.084 / Net I/σ(I): 9.6
Reflection shellResolution: 5.77→6.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.359 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4157 / CC1/2: 0.687 / Rpim(I) all: 0.561 / Rrim(I) all: 1.472 / Rsym value: 1.359 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.77→48 Å / SU ML: 1.3149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 52.9843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.4256 1643 10.9 %
Rwork0.4047 13433 -
obs0.4069 15076 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 362.14 Å2
Refinement stepCycle: LAST / Resolution: 5.77→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20736 0 0 0 20736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003721148
X-RAY DIFFRACTIONf_angle_d0.635228724
X-RAY DIFFRACTIONf_chiral_restr0.04363512
X-RAY DIFFRACTIONf_plane_restr0.00423536
X-RAY DIFFRACTIONf_dihedral_angle_d14.66657404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.77-5.940.42631070.43971020X-RAY DIFFRACTION90.67
5.94-6.140.50911240.46081148X-RAY DIFFRACTION99.61
6.14-6.350.46041180.46371154X-RAY DIFFRACTION99.84
6.35-6.610.4971740.45331076X-RAY DIFFRACTION99.68
6.61-6.910.44971220.4511128X-RAY DIFFRACTION99.92
6.91-7.270.45251490.46121124X-RAY DIFFRACTION99.84
7.27-7.720.47221250.45361139X-RAY DIFFRACTION99.84
7.73-8.320.43271540.42481112X-RAY DIFFRACTION99.84
8.32-9.150.40241530.40231130X-RAY DIFFRACTION99.84
9.15-10.460.38291390.35081118X-RAY DIFFRACTION99.45
10.47-13.130.38011470.35741121X-RAY DIFFRACTION99.06
13.14-480.46161310.41971163X-RAY DIFFRACTION98.1

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