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- PDB-8ctw: Crystal structure of a K+ selective NaK mutant (NaK2K) -Na+,Tl+ c... -

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Basic information

Entry
Database: PDB / ID: 8ctw
TitleCrystal structure of a K+ selective NaK mutant (NaK2K) -Na+,Tl+ complex
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Potassium ion channel / thallium ion / Tl+
Function / homology
Function and homology information


potassium channel activity / membrane
Similarity search - Function
Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THALLIUM (I) ION / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus m1550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM12345 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM141697 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM118217 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)DP2OD028805 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Kinship FoundationSSP-2018-3240 United States
New York Community Trust338034 United States
CitationJournal: To Be Published
Title: Direct visualization of electric field-stimulated ion conduction in a potassium channel
Authors: Lee, B. / White, K.I. / Socolich, M.A. / Klureza, M.A. / Henning, R. / Srajer, V. / Ranganathan, R. / Hekstra, D.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,83027
Polymers21,2812
Non-polymers3,54925
Water90150
1
A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,14148
Polymers42,5624
Non-polymers6,57944
Water724
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
MethodPISA
2
B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,17860
Polymers42,5624
Non-polymers7,61656
Water724
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
MethodPISA
Unit cell
Length a, b, c (Å)67.900, 67.900, 89.384
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
Components on special symmetry positions
IDModelComponents
11A-208-

TL

21A-209-

TL

31A-210-

TL

41A-211-

TL

51B-210-

TL

61B-211-

TL

71B-212-

TL

81B-213-

TL

91B-214-

NA

101A-321-

HOH

111B-316-

HOH

121B-323-

HOH

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Components

#1: Protein Potassium channel protein


Mass: 10640.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus m1550 (bacteria) / Gene: bcere0011_5790 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: C2R3K4
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Tl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NaK2K protein was mixed with 50mM MES pH 6.5/100mM potassium citrate/200mM TlNO3/56%-68% MPD while 50mM MES pH 6.5/100mM potassium citrate/200mM KNO3/56%-68% MPD was used for the reservoir. ...Details: NaK2K protein was mixed with 50mM MES pH 6.5/100mM potassium citrate/200mM TlNO3/56%-68% MPD while 50mM MES pH 6.5/100mM potassium citrate/200mM KNO3/56%-68% MPD was used for the reservoir. Crystal is transferred to 100mM TlNO3/50mM MES (pH 6.0 or 6.5)/100mM sodium citrate/56%-68% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97864 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23618 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 28.381
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.889 / Num. unique obs: 547 / CC1/2: 0.731 / Rsym value: 0.974 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OUF

3ouf


Resolution: 2→48.01 Å / SU ML: 0.1863 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 20.7817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 2399 10.16 %
Rwork0.1799 21218 -
obs0.1817 23617 87.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.94 Å2
Refinement stepCycle: LAST / Resolution: 2→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 137 50 1670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471938
X-RAY DIFFRACTIONf_angle_d0.862673
X-RAY DIFFRACTIONf_chiral_restr0.045321
X-RAY DIFFRACTIONf_plane_restr0.0053312
X-RAY DIFFRACTIONf_dihedral_angle_d18.2572667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.2551690.2146714X-RAY DIFFRACTION48.79
2.04-2.080.2371050.2174761X-RAY DIFFRACTION55.44
2.08-2.130.30091040.1927911X-RAY DIFFRACTION64.32
2.13-2.190.20321190.19341042X-RAY DIFFRACTION71.45
2.19-2.240.21411260.18071070X-RAY DIFFRACTION77.36
2.24-2.310.22161320.18011174X-RAY DIFFRACTION83.08
2.31-2.380.21141530.19071282X-RAY DIFFRACTION88.58
2.39-2.470.21221510.18731377X-RAY DIFFRACTION96.34
2.47-2.570.18771600.16441431X-RAY DIFFRACTION99.38
2.57-2.690.17931660.16191424X-RAY DIFFRACTION100
2.69-2.830.19321740.17051439X-RAY DIFFRACTION100
2.83-30.21460.18251402X-RAY DIFFRACTION99.74
3.01-3.240.18331500.17091456X-RAY DIFFRACTION99.75
3.24-3.560.1721620.17721430X-RAY DIFFRACTION100
3.56-4.080.20751600.16341439X-RAY DIFFRACTION100
4.08-5.140.1711700.16881406X-RAY DIFFRACTION99.87
5.14-48.010.2141520.211460X-RAY DIFFRACTION99.69

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