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- PDB-8k1k: KtrA bound with ATP and sodium -

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Basic information

Entry
Database: PDB / ID: 8k1k
TitleKtrA bound with ATP and sodium
ComponentsKtr system potassium uptake protein A
KeywordsMETAL BINDING PROTEIN / Potassium channel
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
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
ADENOSINE-5'-TRIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChiang, W.T. / Chang, Y.K. / Hu, N.J. / Tsai, M.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB
Authors: Chiang, W.T. / Chang, Y.K. / Hui, W.H. / Chang, S.W. / Liao, C.Y. / Chang, Y.C. / Chen, C.J. / Wang, W.C. / Lai, C.C. / Wang, C.H. / Luo, S.Y. / Huang, Y.P. / Chou, S.H. / Horng, T.L. / Hou, ...Authors: Chiang, W.T. / Chang, Y.K. / Hui, W.H. / Chang, S.W. / Liao, C.Y. / Chang, Y.C. / Chen, C.J. / Wang, W.C. / Lai, C.C. / Wang, C.H. / Luo, S.Y. / Huang, Y.P. / Chou, S.H. / Horng, T.L. / Hou, M.H. / Muench, S.P. / Chen, R.S. / Tsai, M.D. / Hu, N.J.
History
DepositionJul 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8715
Polymers49,8342
Non-polymers1,0373
Water0
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,48320
Polymers199,3348
Non-polymers4,14912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30800 Å2
ΔGint-212 kcal/mol
Surface area74230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.536, 122.536, 83.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 24916.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32080
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES-KOH pH 7.5, 3% PEG 6000, 2.5% 2- methyl-2,4-pentanediol (MPD), 10 mM Thallium(I) acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→28.01 Å / Num. obs: 24361 / % possible obs: 99.6 % / Redundancy: 15.2 % / Biso Wilson estimate: 88.4 Å2 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.043 / Χ2: 1.035 / Net I/σ(I): 50.39
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 5.03 / Num. unique obs: 1243 / CC1/2: 0.97 / CC star: 0.992 / Rrim(I) all: 0.431 / Χ2: 0.817 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→28.01 Å / SU ML: 0.4733 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.7165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2689 2439 10.01 %
Rwork0.2207 21922 -
obs0.2254 24361 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.81 Å2
Refinement stepCycle: LAST / Resolution: 3→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 63 0 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233530
X-RAY DIFFRACTIONf_angle_d0.53594782
X-RAY DIFFRACTIONf_chiral_restr0.0463552
X-RAY DIFFRACTIONf_plane_restr0.0026600
X-RAY DIFFRACTIONf_dihedral_angle_d6.3278470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.060.36761380.35521260X-RAY DIFFRACTION99.57
3.06-3.120.43461480.34881284X-RAY DIFFRACTION100
3.12-3.20.46941460.33841293X-RAY DIFFRACTION99.93
3.2-3.280.371420.34041264X-RAY DIFFRACTION100
3.28-3.360.32721440.31361337X-RAY DIFFRACTION100
3.36-3.460.33821520.25491287X-RAY DIFFRACTION100
3.46-3.570.34211460.28491296X-RAY DIFFRACTION99.93
3.58-3.70.32391500.27571312X-RAY DIFFRACTION100
3.7-3.850.33081480.25061288X-RAY DIFFRACTION100
3.85-4.020.3131400.23411275X-RAY DIFFRACTION100
4.03-4.230.29281480.21981302X-RAY DIFFRACTION100
4.24-4.50.23561480.20211283X-RAY DIFFRACTION99.93
4.5-4.840.2331350.18681272X-RAY DIFFRACTION100
4.85-5.330.23011360.19731338X-RAY DIFFRACTION100
5.33-6.090.30011470.20351283X-RAY DIFFRACTION99.93
6.1-7.640.21961420.20951301X-RAY DIFFRACTION99.86
7.66-28.010.17071290.14641247X-RAY DIFFRACTION95.69
Refinement TLS params.Method: refined / Origin x: -17.9945150793 Å / Origin y: 33.4520000818 Å / Origin z: -34.0827754447 Å
111213212223313233
T0.568439563599 Å20.0870048438668 Å20.0302424519458 Å2-0.729345777546 Å2-0.202832959003 Å2--0.679621716284 Å2
L2.03932253316 °2-0.689881810966 °20.117045906068 °2-3.07815698073 °2-0.959636299259 °2--2.07375386331 °2
S-0.505020478408 Å °-0.100484032684 Å °0.183793739425 Å °0.191517018629 Å °0.225119816956 Å °-0.396544706723 Å °-0.143156056005 Å °-0.343991381949 Å °0.269342506459 Å °
Refinement TLS groupSelection details: all

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