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- PDB-8ctn: Structure of a K+ selective NaK mutant (NaK2K, Laue diffraction, ... -

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Basic information

Entry
Database: PDB / ID: 8ctn
TitleStructure of a K+ selective NaK mutant (NaK2K, Laue diffraction, no electric field)
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Potassium ion channel / EFX / electric field
Function / homologyTwo pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / membrane / : / Potassium channel protein
Function and homology information
Biological speciesBacillus cereus m1550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
Kinship FoundationSSP-2018-3240 United States
New York Community Trust338034 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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,10132
Polymers21,2812
Non-polymers2,82030
Water70339
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)46,33652
Polymers42,5624
Non-polymers3,77548
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)50,06976
Polymers42,5624
Non-polymers7,50772
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)68.816, 68.816, 90.365
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-207-

K

21A-208-

K

31A-209-

K

41A-210-

K

51A-211-

K

61A-212-

K

71B-212-

K

81B-213-

K

91B-214-

K

101B-215-

K

111B-216-

K

121B-217-

K

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


Mass: 118.174 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293.15 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: 289 K / Ambient temp details: room temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.15
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Mar 21, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.151
ReflectionResolution: 2→100 Å / Num. obs: 10684 / % possible obs: 75.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 42.5
Reflection shellResolution: 2→2.09 Å / Mean I/σ(I) obs: 7.67 / Num. unique obs: 562 / % possible all: 32.14

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Precognitiondata reduction
Epinormdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Room temperature NaK2K, monochromatic, SSRL

Resolution: 2.01→21.42 Å / SU ML: 0.1765 / Cross valid method: FREE R-VALUE / σ(F): 2.99 / Phase error: 17.5854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1975 552 5.21 %
Rwork0.1534 10041 -
obs0.1556 10593 74.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 2.01→21.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 171 39 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742039
X-RAY DIFFRACTIONf_angle_d0.85812813
X-RAY DIFFRACTIONf_chiral_restr0.046342
X-RAY DIFFRACTIONf_plane_restr0.0064326
X-RAY DIFFRACTIONf_dihedral_angle_d15.7579714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.210.1654900.12141540X-RAY DIFFRACTION46.39
2.21-2.530.17781490.12982517X-RAY DIFFRACTION75.72
2.53-3.180.1861640.14713010X-RAY DIFFRACTION90.04
3.18-21.420.22291490.17142974X-RAY DIFFRACTION87.5

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