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- PDB-7oq1: NaK S-ELM mutant with Na+ and K+ -

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Basic information

Entry
Database: PDB / ID: 7oq1
TitleNaK S-ELM mutant with Na+ and K+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium channel activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
ACETATE ION / : / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinniberger, S. / Plested, A.J.R.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Research Council (ERC)647895European Union
German Research Foundation (DFG)fg-2518 291198853 Germany
German Research Foundation (DFG)323514590 Germany
German Research Foundation (DFG)446182550 Germany
Citation
Journal: J.Mol.Biol. / Year: 2023
Title: Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors.
Authors: Minniberger, S. / Abdolvand, S. / Braunbeck, S. / Sun, H. / Plested, A.J.R.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJun 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Feb 7, 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)23,40828
Polymers21,5562
Non-polymers1,85326
Water75742
1
A: Potassium channel protein
B: Potassium channel protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)46,81656
Polymers43,1114
Non-polymers3,70552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area17610 Å2
ΔGint-285 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.214, 87.277, 48.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-206-

K

21A-207-

K

31B-203-

K

41B-209-

ACT

51B-209-

ACT

61B-210-

NA

71B-211-

NA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel protein


Mass: 10777.784 Da / Num. of mol.: 2 / Mutation: D66S G67- N68E F69L S70M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_0669 / Plasmid: pQE60 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): NEBExpress Iq / References: UniProt: Q81HW2

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Non-polymers , 7 types, 68 molecules

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


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.01 Å3/Da / Density % sol: 38.8 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES (NaOH) pH 7.5, 47% MPD (2-Methyl-2,4-pentanediol racemate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.85→59.45 Å / Num. obs: 15103 / % possible obs: 99.06 % / Redundancy: 2 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03287 / Rpim(I) all: 0.03287 / Rrim(I) all: 0.04648 / Net I/σ(I): 11.46
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4445 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1357 / CC1/2: 0.693 / CC star: 0.905 / Rpim(I) all: 0.4445 / Rrim(I) all: 0.6286 / % possible all: 91.07

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+86 / Resolution: 1.85→59.45 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1862 1516 10.04 %
Rwork0.1597 13584 -
obs0.1624 15100 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→59.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 118 42 1634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211634
X-RAY DIFFRACTIONf_angle_d0.82432224
X-RAY DIFFRACTIONf_chiral_restr0.0627273
X-RAY DIFFRACTIONf_plane_restr0.0069266
X-RAY DIFFRACTIONf_dihedral_angle_d12.7293545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.29371220.25251110X-RAY DIFFRACTION90.52
1.91-1.980.27471420.21321231X-RAY DIFFRACTION99.56
1.98-2.060.22841210.17941228X-RAY DIFFRACTION99.93
2.06-2.150.18781380.15831226X-RAY DIFFRACTION100
2.15-2.260.20581510.1541218X-RAY DIFFRACTION99.85
2.26-2.410.20221280.16111230X-RAY DIFFRACTION99.78
2.41-2.590.16651450.13431245X-RAY DIFFRACTION100
2.59-2.850.16941360.13621248X-RAY DIFFRACTION100
2.85-3.270.16351400.13411247X-RAY DIFFRACTION100
3.27-4.110.16581420.14091270X-RAY DIFFRACTION99.93
4.12-59.450.18471510.1811331X-RAY DIFFRACTION99.93
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)
12.88519732654-0.2642262481060.4073251824424.29447123166-0.7380657037352.50482640822-0.119257758740.01254360369310.0939418524373-0.1017067439930.0845687161312-0.290169921452-0.124726392980.03487397005430.03848221860820.1134873020850.005686858947760.003895409071180.163924871162-0.02655953517170.11690579986816.559966012321.1266760634-6.0459207215
24.97515704621-3.787390830664.574978832774.82679788996-5.372260969116.034898701990.498621555033-0.0468398056027-0.958783687004-0.5952311831420.1389500795620.8078985303911.01408004279-0.0788053431321-0.5964251759050.303670632846-0.0238041667394-0.02038352651950.250264429518-0.02243429807050.3151613357065.0522989934811.2098798421-6.30002297996
33.373319287552.99130844769-4.67830822116.38413623552-6.755830009928.500252787820.04896960658580.2080476421910.1910878044950.003171217066080.2075984908020.0637717538543-0.213456142036-0.39490456381-0.3108759334980.1934963023660.00827206528498-0.0245315631060.230504307627-0.01771567275920.19297315940710.115018098727.7157028718-10.406035555
44.36649291032-2.38913983490.4417576799097.17269332897-2.267495415564.112187602920.202571186950.4185283569540.521539466012-0.267720489624-0.299742756502-0.398093847818-0.270343291661-0.1265509453950.1281813192270.20002758141-0.003372950649830.04839897462430.2551107439620.0382181472370.1942213691438.8317860760224.4055913353-29.4689399354
53.48641555704-2.89910823683-1.820631886937.367734729752.03247428333.49554800612-0.006386811535280.16651644462-0.22777737285-0.340266678566-0.01004768055250.1681150169070.118993261723-0.1378185748470.04155890076590.170784050264-0.02094819617060.01542945301780.204964101711-0.006796386838050.1751990712214.7467521430812.3540116634-25.4588249914
65.76846404393-5.87419691328-2.777283238656.028098779632.823899428531.29597665052-0.4417490777870.228983004699-1.006316054450.46233409012-0.02120229973420.7615433756050.426339077994-0.09930404500470.4358346006870.264632802244-0.02984294174470.03801344105510.226212484848-0.004459877319910.3470419037445.5870647095811.2959893051-17.2362948665
78.66351970549-5.467903019543.779959789227.72102798023-2.199900758693.92707886032-0.1595381581210.01613376697970.604933252918-0.07166063300450.00622492691375-0.15335497388-0.211115593231-0.04476096545350.1494940310350.139409430099-0.02980131500680.02806540731990.1666250786730.004581532956890.1387364254778.0631355593924.5364809573-20.4581949219
89.0268760772-6.057149965221.046702105096.89554185629-0.2339205732336.06537970529-0.202908904561-0.42036674641-0.271350897483-0.3544897248430.2827475959290.362201670179-0.039152915179-0.221810967935-0.08010497066410.271744769708-0.0167725414966-0.02277065036730.2672102424190.03110356178930.303375062581-15.481073115738.4245601745-28.553373573
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 61 )AA19 - 611 - 43
22chain 'A' and (resid 62 through 72 )AA62 - 7244 - 54
33chain 'A' and (resid 73 through 110 )AA73 - 11055 - 92
44chain 'B' and (resid 21 through 45 )BB21 - 451 - 25
55chain 'B' and (resid 46 through 61 )BB46 - 6126 - 41
66chain 'B' and (resid 62 through 72 )BB62 - 7242 - 52
77chain 'B' and (resid 73 through 100 )BB73 - 10053 - 80
88chain 'B' and (resid 101 through 113 )BB101 - 11381 - 93

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