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- PDB-7oq2: NaK S-DI mutant soaked in Na+ -

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Basic information

Entry
Database: PDB / ID: 7oq2
TitleNaK S-DI mutant soaked in Na+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN
Function / homologyTwo pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / metal ion binding / identical protein binding / membrane / : / Potassium channel protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)23,80728
Polymers21,4392
Non-polymers2,36826
Water1,71195
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)47,61556
Polymers42,8794
Non-polymers4,73652
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area19940 Å2
ΔGint-548 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.204, 88.173, 49.389
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-215-

NA

21A-216-

NA

31A-217-

NA

41A-218-

K

51A-219-

K

61B-205-

NA

71B-343-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel protein


Mass: 10719.641 Da / Num. of mol.: 2 / Mutation: D66S G67- N68D F69I
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 , 5 types, 121 molecules

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


Mass: 118.174 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM KCl, 100 mM HEPES (KOH) pH 7.5, 62% MPD (2-Methyl-2,4-pentanediol racemate) - soaked in 100 mM NaCl, 100 mM Tris-HCl pH 8.0, 50% MPD

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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: 1.7→59.73 Å / Num. obs: 19895 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 21.96 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06674 / Rpim(I) all: 0.06674 / Rrim(I) all: 0.09439 / Net I/σ(I): 4.46
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2 % / Rmerge(I) obs: 0.9783 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1966 / CC1/2: 0.596 / CC star: 0.864 / Rpim(I) all: 0.9783 / % possible all: 99.69

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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: 1.7→59.73 Å / SU ML: 0.2224 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1969 9.91 %
Rwork0.1858 17893 -
obs0.1904 19862 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 152 95 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941629
X-RAY DIFFRACTIONf_angle_d0.70832232
X-RAY DIFFRACTIONf_chiral_restr0.0504280
X-RAY DIFFRACTIONf_plane_restr0.0054247
X-RAY DIFFRACTIONf_dihedral_angle_d13.0903537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.34941260.32341244X-RAY DIFFRACTION99.64
1.74-1.790.30681400.30381257X-RAY DIFFRACTION99.5
1.79-1.840.33851450.28921255X-RAY DIFFRACTION99.64
1.84-1.90.33921360.26171279X-RAY DIFFRACTION99.93
1.9-1.970.28111410.23921246X-RAY DIFFRACTION99.78
1.97-2.050.25761320.21651274X-RAY DIFFRACTION99.65
2.05-2.140.241470.19341269X-RAY DIFFRACTION99.93
2.14-2.250.23191440.17911256X-RAY DIFFRACTION99.86
2.25-2.40.22641450.17541275X-RAY DIFFRACTION99.86
2.4-2.580.22821430.16511272X-RAY DIFFRACTION99.86
2.58-2.840.2121390.1511280X-RAY DIFFRACTION99.93
2.84-3.250.17661400.1581295X-RAY DIFFRACTION100
3.25-4.10.18351390.151321X-RAY DIFFRACTION99.86
4.1-59.730.24631520.18541370X-RAY DIFFRACTION99.8
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)
12.392051224750.38136533524-1.564779355222.398518040051.711710028522.707031026860.1262458508470.9814764151650.577129666336-0.2230711556920.137024604177-0.75937920644-0.9696202477650.385802184465-0.3287959747020.333164287495-0.009027725590460.009912005454670.2907537507910.01405610750860.39037021666919.616441180535.8412571415-9.23574700677
27.974433170195.13737211017-3.126732401453.86373067583-3.343045253375.30358195424-0.1876042971730.197861416076-0.1284643867990.299272840934-0.0492843432862-0.165077645751-0.0454274119863-0.1013315137310.1970063018120.192208226206-0.00391363407527-0.05463388898830.2000963994030.03732613042830.16064403302118.284291160326.6810374851-4.4034429186
32.77637159260.42842635389-2.49567161249.5622209122-5.676757179465.180029664910.181619074755-0.124386602443-0.2102363891420.214215316436-0.1026180653150.283253901899-0.1874670840440.1806234338380.01551254081870.17538484722-0.00982740422433-0.02399140034080.300951015871-0.03342924225270.14144351491217.968074696717.9091156086-2.33537029321
48.95412720231-0.497509444082-3.742423667265.391399127413.299050327076.53332394178-0.32640756832-0.868896884483-0.5680938042160.2230049082710.2566846095040.1726233063810.539044801890.4708776954770.05961705326580.2079398651990.0323085613762-0.0163553953530.219300026140.04918675655720.28430216110714.153613510910.24591119270.918724546582
56.31301261331.77517186321-0.7863223984463.98166792958-5.881137968039.276244946380.0878287583590.1331521141970.422166473623-0.5124961162960.03279554765270.1245910861380.727508907785-0.433106317427-0.123939975040.210668128918-0.000717851005718-0.03895732215090.1761885340310.001435340757010.22925297892717.20309361598.48706623134-7.95807599271
65.89548253661-1.927084799631.670719089593.92350380694-0.9393789502874.718364607010.02652671226230.160126851674-0.372865955002-0.0392552999171-0.08971139800130.2440237120920.2550191184630.1068493573620.07715441842070.1537665222520.01445518933850.007136127098970.141443231431-0.0101504299230.1667745455728.1771280731515.3567465323-8.91566392729
74.572792146793.142337113762.304279436894.01023748375-0.5777835492923.685498511360.175549174759-0.285340058904-0.6875026196570.424107415594-0.0205237615946-0.2811698308590.411298545014-0.444161074783-0.217231737680.239287102252-0.040253634179-0.003550604480850.2672393850030.08992556288350.2934369237326.842957177158.882126614014.27742361972
89.93463962592.567271519-1.211396798775.72645398443-1.864060383647.59323591619-0.08613668548270.0500123917386-0.3032920727840.2724705434810.04866003825060.358053703506-0.139531847647-0.26879321088-0.002127807136640.1635346851620.0182706600496-0.02018170554280.1723843478230.003025477302760.1559940405536.5031500908317.42477412412.67851565302
96.77162022072.29605206427-2.691324541145.34521887139-4.038833284863.27814210481-0.0447333188656-0.0882952629791-0.16463119038-0.03800253759520.1505874562760.0338234202023-0.4080474604670.468239670575-0.08220879217830.2367585434760.006335944932280.00368770152160.184274820846-0.03027249806440.2031881347227.0782114472726.7500553147-4.15412732378
107.809966268850.45732485453-1.345253628632.15608242562-2.529984464937.58867473416-0.06210898287270.291738965650.954674687314-0.1781829916660.3196055979740.374484106475-0.689544281959-0.351968802285-0.1137076164370.2974191922830.0386119265115-0.01155861260480.2135033476290.02653767870480.23864864565111.786222498532.8358584594-13.0740033783
116.00630416759-1.371018335120.663795377555.6851527314-5.831539852476.0594692856-0.292956218856-0.0810523706168-0.480439291226-0.09854039776530.4966562063560.039742601493-0.357519520884-0.430879849119-0.3077860463350.269489629524-0.001130646695120.01504320135420.319727490494-0.006559793332530.29467904813614.41989730635.0427166313-20.8702683114
129.95556424055-4.88109656561-4.863880674314.360753540736.150925049639.679681372651.184946124620.4577199952390.639754185544-0.638343498637-0.9038945521760.605408725313-1.4337344256-0.24177894178-0.2579263170210.4633044316430.06247958988010.09725867222940.319162000966-0.0297688018910.3940534652615.58838251139.0376304229-29.1962726272
133.7295310272-1.01355033733.793363707032.23785623926-1.786564084744.55256920472-0.3375167783740.45789252542-0.255174561010.02806493452850.3209607541780.0730331577505-2.22473359098-0.765091429420.2217472875690.6142802735880.0964022020917-0.06701919608860.5130813611380.01393039606350.480852533283.4531585867840.0964193178-31.3782818455
145.647132170632.69844819287-5.110850942481.71352589744-2.52340132664.642934736340.4154492780081.019590334520.843747390148-1.426374621670.1451229905570.0750282190439-1.57575031619-0.457815593375-0.4131916681860.4462867779390.02852350295840.03340456839210.2556059070760.05435804533570.3220385544276.430602788432.8554287213-31.4601911251
155.93515247919-5.82760934137-2.189079904739.22429884418-0.5575832828995.416390336550.445456646790.7006693234090.222439804319-0.539691763811-0.479394126457-0.253667610055-0.1949348536970.05074436144640.09156837276830.1824221687350.006131943681060.01791659409750.2305760500180.001784057258230.1551315482079.1654873673123.3836107719-29.7721408228
166.86321399054-2.53746219737-0.1297114293863.556326275610.7906007087181.772346446390.1600717788760.0907249016871-0.312500752401-0.210957824795-0.0832955456139-0.092293061286-0.01825215616240.0495588361394-0.0769650800220.167874857557-0.01476867143760.01365307430730.182914581826-0.01857761179760.1402271385877.198045030711.8302476063-26.8920357126
176.0196412042-1.61272263055-0.58252810951.100524621520.3210333438484.096430580110.09689772697130.299130977358-0.102408325275-0.02794399377910.104782153111-0.0149770483935-0.01989830411430.283049008043-0.08432118872970.173021700905-0.02289179619450.01066508321570.225875419537-0.04736645656730.181085059892.4388421784920.0993281829-18.1045136639
187.15572244043-6.61419579089-4.873467998656.157586091794.234211995437.63856872093-0.0552225488081.09276781169-2.16531268769-0.326489207497-0.642694684970.650575611345-0.298911929743-0.6488433817680.7068198079370.318930102572-0.04506058589350.06534224069060.300780829037-0.05709519537470.4600441743536.155381627078.09230974556-17.7606517714
191.71537158329-1.949727054131.999057938722.34167608423-2.397922460432.54351038296-0.0739956907350.031163202444-0.1026340152510.04974148192180.0146331492848-0.03817214043110.04132537086450.139066620990.05095986140470.174379555015-0.01077582715110.03107030951660.217143477934-0.01133734046720.19011253135115.35916288215.0485600128-18.6604755045
204.81002418398-4.431899242526.318161370125.05283412923-5.383094868038.39999983294-0.453925189908-0.05123629977490.8284315408450.266102170779-0.0787575044343-0.253525064492-0.296580484996-0.2581696717410.4754936839450.211643507736-0.00993205648959-0.001557795310260.2290329769040.01473728761770.2585575950494.8667069892929.6729709167-20.9182382718
217.09988636231-2.83568498474-0.7653961354173.1633032186-0.9297885036733.05751001741-0.1993939420640.07075169420561.157173296170.296597474920.293074692036-0.75994224380.6866691562570.272878319335-0.244997413090.24111016080.0568871234939-0.05819530302110.2295348611870.009549579756170.375848676773-8.3285446801836.5789207689-27.1227867681
222.01490248385-0.05447947176064.919571087852.02526169715-1.927587608916.78179971291-0.3189161142940.0171479651779-0.221491304627-0.5628169055370.110349873741-0.147819578227-0.122908756312-0.3180970860970.2428408838660.2559481522120.0297679899241-0.02510180893330.320586575612-0.02863605635840.362243088735-20.084015216340.5413620775-30.003541314
232.14582997356-0.3329867224471.42339880871.78205000827-2.340725456754.27736200146-0.2189035901240.3110950525880.099394893456-0.3603629533-0.105468771659-0.09857006894110.430503571106-0.07989443955060.05665129804851.679664390660.328563329946-0.04169114530690.5742545499580.2362759733660.54406566560314.102677441942.9253653187-32.9255776146
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 21:28)AA21 - 281 - 8
22(chain A and resid 29:34)AA29 - 349 - 14
33(chain A and resid 35:40)AA35 - 4015 - 20
44(chain A and resid 41:47)AA41 - 4721 - 27
55(chain A and resid 48:52)AA48 - 5228 - 32
66(chain A and resid 53:69)AA53 - 6933 - 49
77(chain A and resid 70:75)AA70 - 7550 - 55
88(chain A and resid 76:82)AA76 - 8256 - 62
99(chain A and resid 83:91)AA83 - 9163 - 71
1010(chain A and resid 92:96)AA92 - 9672 - 76
1111(chain A and resid 97:103)AA97 - 10377 - 83
1212(chain A and resid 104:108)AA104 - 10884 - 88
1313(chain B and resid 19:24)BB19 - 241 - 6
1414(chain B and resid 25:29)BB25 - 297 - 11
1515(chain B and resid 30:38)BB30 - 3812 - 20
1616(chain B and resid 39:59)BB39 - 5921 - 41
1717(chain B and resid 60:65)BB60 - 6542 - 47
1818(chain B and resid 66:71)BB66 - 7148 - 53
1919(chain B and resid 72:83)BB72 - 8354 - 65
2020(chain B and resid 84:96)BB84 - 9666 - 78
2121(chain B and resid 97:106)BB97 - 10679 - 88
2222(chain B and resid 107:113)BB107 - 11389 - 95
2323(chain A and resid 109:111)AA109 - 11189 - 91

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