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- PDB-8ctt: Crystal structure of a K+ selective NaK mutant (NaK2K) at 100K -

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Basic information

Entry
Database: PDB / ID: 8ctt
TitleCrystal structure of a K+ selective NaK mutant (NaK2K) at 100K
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Potassium ion channel / anomalous
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
: / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus m1550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)22,93322
Polymers21,2812
Non-polymers1,65220
Water88349
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)45,23540
Polymers42,5624
Non-polymers2,67336
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)46,49648
Polymers42,5624
Non-polymers3,93444
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)67.765, 67.765, 88.385
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-205-

K

21A-206-

K

31A-207-

K

41A-208-

K

51B-208-

K

61B-209-

K

71B-210-

K

81B-211-

K

91A-328-

HOH

101B-320-

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.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.45865 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45865 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 21211 / % possible obs: 99.5 % / Redundancy: 43.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 111
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 32.4 % / Mean I/σ(I) obs: 8.706 / Num. unique obs: 630 / CC1/2: 0.981

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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: 2.05→33.88 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 20.047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.189 1717 8.1 %
Rwork0.1621 19490 -
obs0.1642 21207 86.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.39 Å2
Refinement stepCycle: LAST / Resolution: 2.05→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 97 49 1613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01061918
X-RAY DIFFRACTIONf_angle_d0.9552638
X-RAY DIFFRACTIONf_chiral_restr0.054319
X-RAY DIFFRACTIONf_plane_restr0.0072313
X-RAY DIFFRACTIONf_dihedral_angle_d16.1591663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.2017770.1883894X-RAY DIFFRACTION47.34
2.12-2.180.2195880.16651151X-RAY DIFFRACTION59.34
2.18-2.260.17031320.13911288X-RAY DIFFRACTION70.89
2.26-2.350.15691200.16051512X-RAY DIFFRACTION80.51
2.35-2.460.23761530.16191638X-RAY DIFFRACTION87.2
2.46-2.590.15941580.14851793X-RAY DIFFRACTION94.94
2.59-2.750.16671420.15561850X-RAY DIFFRACTION98.61
2.75-2.960.19281780.16541892X-RAY DIFFRACTION99.9
2.96-3.260.20021900.15721847X-RAY DIFFRACTION100
3.26-3.730.19921590.15691864X-RAY DIFFRACTION99.9
3.73-4.70.16611460.13861904X-RAY DIFFRACTION99.81
4.7-33.880.20661740.20121857X-RAY DIFFRACTION98.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.564628509980.292433789872-0.90378952322.813087763560.6524054704411.931454799740.0742980545814-0.420722657082-0.340371474590.464353914403-0.1621807055350.02011413728370.5712790082080.1117332108130.0863048038170.289977574105-0.05257815967730.07051124485270.1184766064220.01935623624720.24333796468-2.899-18.26721.861
23.88360869289-0.5964225868221.083861798072.895814149860.008900934000052.81162303536-0.124388025487-0.7440677741250.0246410008480.488238480207-0.08974725589960.1235792446740.276084419824-0.2697328079140.2118199592030.214488273734-0.02895645390730.07977043996880.2029249872770.00310083478450.17887918144-5.665-10.21726.18
33.797312059110.557926465935-2.737207899614.766503914810.7859553248162.27437637916-0.335878026324-0.7435520717310.202691888263-0.0820048379410.260261006537-0.151113408339-0.4215616452050.09783010181220.0757577411320.5785673376320.0719163759177-0.06048339279550.456193214070.07758146235310.26691965232318.921-11.33938.982
43.006772232930.06758649904980.08784363648253.51795669405-0.2514781470592.279501207890.103700313391-0.345270134312-0.1942459677910.239655351950.06128134623830.3192263977760.260263474524-0.34718270257-0.1653106989530.168492427181-0.05494857007130.06397924337290.1707463240720.05073834750750.19671855807-14.585-10.951-20.116
52.96699750173-1.518136514641.709548011423.50430565374-1.463006997672.907999107870.124207087562-0.195938335579-0.139008995666-0.0381393344617-0.154532037634-0.09818770797420.453433584493-0.01589165718440.03033183544560.170402364162-0.01795467074790.02348081029510.1338681934240.03262518798050.167829670708-5.967-9.669-23.63
62.36246721308-3.24878887490.9254635092299.97117667792-4.022635217462.495712668470.3224925062650.0334575945954-0.0186193713447-0.472418093319-0.001869646614260.3959197165720.0547211492823-0.174978511399-0.3209921650220.2332301944780.05552016469690.005430036603820.141730948464-0.02394550982990.253590345686-19.73311.61-37.13
72.240037493560.1237094187120.9322327779722.2989031247-0.6973667582713.30331652774-0.05987611960340.00148095303926-0.349951120001-0.137072198512-0.0479411794748-0.05308157813480.2931762786110.134972422350.1073255688560.09220695103270.01370499303110.03589773276420.0731261011959-0.0001244552232290.1540737434950.212-6.2416.946
83.478511161780.6832850632330.8660076120583.80171828032-0.8948037247461.44046164961-0.124398168311-0.520705456441-0.1948631363910.5418231873430.03855876454920.2062388148870.0193593756745-0.2465208281940.0854546912020.18042990490.004581056523330.03349083710710.1756363510080.01694447744380.115080041668-5.412-2.872-15.035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:58 )A20 - 58
2X-RAY DIFFRACTION2( CHAIN A AND RESID 74:101 )A74 - 101
3X-RAY DIFFRACTION3( CHAIN A AND RESID 102:111 )A102 - 111
4X-RAY DIFFRACTION4( CHAIN B AND RESID 20:58 )B20 - 58
5X-RAY DIFFRACTION5( CHAIN B AND RESID 74:101 )B74 - 101
6X-RAY DIFFRACTION6( CHAIN B AND RESID 102:113 )B102 - 113
7X-RAY DIFFRACTION7( CHAIN A AND RESID 59:68 )A59 - 68
8X-RAY DIFFRACTION8( CHAIN B AND RESID 59:68 )B59 - 68

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