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- PDB-8ctu: Crystal structure of a K+ selective NaK mutant (NaK2K) at Room te... -

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Basic information

Entry
Database: PDB / ID: 8ctu
TitleCrystal structure of a K+ selective NaK mutant (NaK2K) at Room temperature
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Potassium ion channel / anomalous / room temperature
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
beta-D-galactopyranose / : / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus m1550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.1Apr 3, 2024Group: 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)22,70717
Polymers21,2812
Non-polymers1,42615
Water57632
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)43,66024
Polymers42,5624
Non-polymers1,09820
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)47,16844
Polymers42,5624
Non-polymers4,60640
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)68.914, 68.914, 90.324
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-302-

K

21A-303-

K

31A-304-

K

41A-305-

K

51B-206-

K

61B-207-

K

71B-208-

K

81B-209-

K

91A-417-

HOH

101B-315-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 45 molecules

#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM KCl, 200mM potassium citrate tribasic monohydrate, 100mM MES (pH 6.0 or 6.5), 56%-68% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 292 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.4938 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4938 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 49726 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.53 Å2 / Rsym value: 0.087 / Net I/σ(I): 21.392
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.156 / Num. unique obs: 2467 / CC1/2: 0.743 / Rsym value: 0.563 / % possible all: 100

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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: Room temperature monochromatic NaK2K structure

Resolution: 1.65→48.73 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.8442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1792 3912 7.87 %
Rwork0.1628 45811 -
obs0.1642 49723 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 83 32 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621933
X-RAY DIFFRACTIONf_angle_d0.95512662
X-RAY DIFFRACTIONf_chiral_restr0.0536335
X-RAY DIFFRACTIONf_plane_restr0.0064321
X-RAY DIFFRACTIONf_dihedral_angle_d15.8293685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.28891560.2811619X-RAY DIFFRACTION99.94
1.67-1.690.3041260.25451644X-RAY DIFFRACTION99.94
1.69-1.710.25921780.23381622X-RAY DIFFRACTION99.45
1.71-1.740.2161350.22241630X-RAY DIFFRACTION99.1
1.74-1.760.26921120.19931661X-RAY DIFFRACTION99.11
1.76-1.790.21631500.18411630X-RAY DIFFRACTION100
1.79-1.820.2061520.18561620X-RAY DIFFRACTION100
1.82-1.850.19991260.19111712X-RAY DIFFRACTION100
1.85-1.880.23241820.19221561X-RAY DIFFRACTION99.89
1.88-1.910.1807980.19561699X-RAY DIFFRACTION99.39
1.91-1.950.19011400.17441634X-RAY DIFFRACTION99.16
1.95-1.990.20071370.16071564X-RAY DIFFRACTION96.37
1.99-2.030.16931370.14991655X-RAY DIFFRACTION99.45
2.03-2.080.17261420.13581664X-RAY DIFFRACTION100
2.08-2.130.17031420.13921607X-RAY DIFFRACTION100
2.13-2.190.12681400.13961633X-RAY DIFFRACTION100
2.19-2.250.16041410.13251625X-RAY DIFFRACTION99.94
2.25-2.330.16741180.13611709X-RAY DIFFRACTION99.84
2.33-2.410.14271390.14571586X-RAY DIFFRACTION96.37
2.41-2.50.15541240.14211623X-RAY DIFFRACTION99.04
2.51-2.620.14351380.12131655X-RAY DIFFRACTION100
2.62-2.760.14051540.1381674X-RAY DIFFRACTION100
2.76-2.930.16061410.13711614X-RAY DIFFRACTION99.94
2.93-3.160.16291420.14871653X-RAY DIFFRACTION99.61
3.16-3.470.12391280.1451605X-RAY DIFFRACTION97.25
3.47-3.970.16121540.15151613X-RAY DIFFRACTION100
3.98-50.17921540.15871638X-RAY DIFFRACTION99.83
5.01-48.730.26481260.2371661X-RAY DIFFRACTION98.78

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