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- PDB-5but: Crystal structure of inactive conformation of KtrAB K+ transporter -

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Basic information

Entry
Database: PDB / ID: 5but
TitleCrystal structure of inactive conformation of KtrAB K+ transporter
Components
  • Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
  • Ktr system potassium uptake protein B
KeywordsMEMBRANE PROTEIN / membrane protein complex
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.97 Å
AuthorsVieira-Pires, R.S. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
FCTFCOMP-01-0124-FEDER-028115 (PTDC/BBB-BEP/2017/2012) Portugal
CitationJournal: Plos Biol. / Year: 2016
Title: Dissecting the Molecular Mechanism of Nucleotide-Dependent Activation of the KtrAB K+ Transporter.
Authors: Szollosi, A. / Vieira-Pires, R.S. / Teixeira-Duarte, C.M. / Rocha, R. / Morais-Cabral, J.H.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B
K: Ktr system potassium uptake protein B
L: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,94312
Polymers320,7878
Non-polymers1564
Water0
1
A: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A,Ktr system potassium uptake protein A
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,5498
Polymers224,4716
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Ktr system potassium uptake protein B
L: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3944
Polymers96,3162
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)307.060, 79.410, 205.650
Angle α, β, γ (deg.)90.000, 98.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ktr system potassium uptake protein A,Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 32038.717 Da / Num. of mol.: 4 / Fragment: regulatory domain,regulatory domain
Mutation: truncation of C-terminal domain,truncation of C-terminal domain
Source method: isolated from a genetically manipulated source
Details: KtrA delta C is a fusion of two N-terminal domains of KtrA through the linker LEGS. It also includes a C to V mutation.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrA, yuaA, BSU31090 / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32080
#2: Protein
Ktr system potassium uptake protein B / K(+)-uptake protein KtrB


Mass: 48158.039 Da / Num. of mol.: 4 / Fragment: membrane protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrB, yubG, BSU31100 / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32081
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl, 16-22% PEG 400, 100-200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 5.97→200 Å / Num. all: 12628 / Num. obs: 12628 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/av σ(I): 8.56 / Net I/σ(I): 10.2 / Num. measured all: 42979
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
5.97-6.33.30.80.9595317900.5190.8221.696.3
6.3-6.683.40.5561.4598817480.3480.5562.498.6
6.68-7.143.50.3632.1562516150.2270.3633.599.4
7.14-7.713.50.2273.4531215210.1420.2275.199.2
7.71-8.453.50.126.3501814210.0750.12999.4
8.45-9.453.40.06710.7442612830.0420.06714.699.5
9.45-10.913.30.04614.8381811530.0290.04620.999.5
10.91-13.363.30.0416.432339710.0260.0423.598.7
13.36-18.893.30.03617.925327680.0230.03625.499.8
18.89-58.34530.0312010743580.020.03129.679.2

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
CNSDENRrefinement
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KtrB from 4J7C and KtrA-deltaC from 2HMS

4j7c

2hms


Resolution: 5.97→200 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.339 2316 9.5 %Random selection
Rwork0.325 21289 --
obs-12628 96.7 %-
Solvent computationBsol: 261.776 Å2
Displacement parametersBiso max: 342.98 Å2 / Biso mean: 342.9982 Å2 / Biso min: 342.98 Å2
Baniso -1Baniso -2Baniso -3
1--142.742 Å20 Å2-25.032 Å2
2--58.294 Å20 Å2
3---84.448 Å2
Refinement stepCycle: final / Resolution: 5.97→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21476 0 4 0 21480
Biso mean--342.98 --
Num. residues----2796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.97-6.190.50282600.4541978223891.3
6.19-6.440.39782060.40972145235196.6
6.44-6.730.43692480.39112123237196.8
6.73-7.080.43372300.36752158238897.7
7.08-7.530.38372110.35962137234897.7
7.53-8.110.35442260.3412233245999.1
8.11-8.930.29622420.27092178242099.3
8.93-10.220.25912660.24322124239098.3
10.22-12.870.30512260.24642160238698.3
12.87-500.010.36352010.40142053225492.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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