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- PDB-8a35: NaK C-DI mutant with Rb+ and Na+ -

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Basic information

Entry
Database: PDB / ID: 8a35
TitleNaK C-DI mutant with Rb+ and 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 / RUBIDIUM ION / Potassium channel protein
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Feb 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)22,73217
Polymers21,4712
Non-polymers1,26115
Water30617
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)44,75628
Polymers42,9434
Non-polymers1,81324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area8970 Å2
ΔGint-143 kcal/mol
Surface area18580 Å2
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)46,17440
Polymers42,9434
Non-polymers3,23136
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
Buried area11410 Å2
ΔGint-242 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.062, 68.062, 90.268
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-201-

RB

21A-202-

RB

31A-205-

NA

41A-206-

NA

51B-201-

RB

61B-202-

RB

71B-208-

NA

81B-209-

NA

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Components

#1: Protein Potassium channel protein


Mass: 10735.706 Da / Num. of mol.: 2 / Mutation: D66C G67- N68D F69I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (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
#2: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.42 Å3/Da / Density % sol: 49.2 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES (NaOH) pH 7.5, 5% PEG 4000, 30% 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: BESSY / Beamline: 14.1 / Wavelength: 0.815 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.05→34.03 Å / Num. obs: 24525 / % possible obs: 96.45 % / Redundancy: 2.4 % / Biso Wilson estimate: 48.9 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.031 / Rrim(I) all: 0.052 / Net I/σ(I): 12.43
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2442 / CC1/2: 0.41 / CC star: 0.763 / Rpim(I) all: 0.6391 / % possible all: 96.71

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+86 / Resolution: 2.05→34.03 Å / Cross valid method: FREE R-VALUE / σ(F): 35.66 / Phase error: 27.181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: twin refinement: twin law: -h,k,-l
RfactorNum. reflection% reflection
Rfree0.217 1278 5.21 %
Rwork0.1923 23247 -
obs0.2147 24525 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.65 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 64 17 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721489
X-RAY DIFFRACTIONf_angle_d0.53852035
X-RAY DIFFRACTIONf_chiral_restr0.0405260
X-RAY DIFFRACTIONf_plane_restr0.0031235
X-RAY DIFFRACTIONf_dihedral_angle_d3.8879194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.130.33461380.34112582X-RAY DIFFRACTION89.72
2.13-2.230.33741330.31692504X-RAY DIFFRACTION90.89
2.23-2.340.32241340.30312572X-RAY DIFFRACTION90.63
2.35-2.490.31621380.28172627X-RAY DIFFRACTION92.96
2.49-2.680.25441390.23352625X-RAY DIFFRACTION92.14
2.68-2.950.24251330.22762568X-RAY DIFFRACTION90.87
2.96-3.380.21451410.20262647X-RAY DIFFRACTION93.24
3.38-4.260.18451330.18322562X-RAY DIFFRACTION90.85
4.26-34.030.22721400.19642609X-RAY DIFFRACTION91.26
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)
11.066493388720.23100893543-0.2341499556651.567675570990.01515171747233.14880238381-0.1242450847180.289345958894-0.548040485419-0.3161381907090.103487034058-0.1392077120110.0469894832956-0.5139847485390.05209622654610.301793135942-0.0488655733172-0.006061583366720.389175243452-0.1307019055930.76618831399521.827674685419.31530291925.67024637592
22.417295282650.2873509986590.2486943071843.788992627451.353909177584.61598799936-0.1627637290520.2611631452780.187149804185-0.09446278911880.8509165942970.799700426201-0.275434727251.24067066943-0.6100557954690.3878600780980.0122470506856-0.03615052146460.421304503258-0.1104142929360.70070184222727.127759246422.8701371283-2.14829450644
31.34174016022-0.6491632121671.050653209450.9597227523-0.9978286853671.194179940740.3076924964010.0219136319432-0.342767580644-0.413356353358-0.02813411321680.02420155466360.3589729148460.00027431536609-0.168939957030.3429587438130.0415825019158-0.05552804601240.393185863351-0.05257889696360.65289004868629.406090596425.49384903178.12388955966
40.352448703984-0.254759404646-0.7224613298870.7744507427910.8519022072895.27203188838-0.5512434956090.0263747331121-0.0991070910824-0.181508448331-0.5454116706490.547151764616-0.2096283643120.01147896290471.017303708340.386711266015-0.0418963035683-0.01205417751840.3525034833820.06821114741080.77764932373919.27515411934.276703834562.50172108772
50.4987834191890.03151485813580.2409072518420.8666938098030.1659520627570.616165087012-0.160729832274-0.1559401587990.5231628544790.0310281972104-0.1935045034030.2994949972250.005109712645320.02149577798580.2322023870420.3090011598510.0205276319517-0.04116165831080.3297061567450.01303749990630.60169133796711.04105981453.2266510970314.8185306937
61.955471971710.449796060866-0.05129297400011.467020165270.8292960338921.56360141857-0.1960845253730.374791700648-0.323755149631-0.5741886348620.004032306869860.340772639774-0.3234787579520.2013689828250.04810578339780.376971325583-0.03090840669320.02829379627660.3690772281110.04936488577540.7885255427149.908958531865.885241321752.12829651337
72.534752736571.052342256520.3761732209591.947556797391.214131832543.87987527399-0.152534802555-0.299586512534-0.06285973347210.08177421678650.1342362107580.400768330875-0.551574396525-0.403027410693-0.09153326652410.5467338544420.09591776758320.04645820045510.737458096168-0.07505050889560.51333192733712.1974950723-14.7895985269-10.1506103704
81.869227561190.679996765179-0.6608548563851.44184062635-0.6488117849170.3749051091660.2397940569-0.25995842662-0.0212542257394-0.119469527655-0.00430849579436-0.34952322175-0.1418180589230.374640040119-0.09886732698170.3071199890260.01144339926210.288241700521.63827416757-0.6209109089531.286158718999.38694547069-24.2218257405-12.2559105728
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 49 )AA20 - 491 - 30
22chain 'A' and (resid 50 through 61 )AA50 - 6131 - 42
33chain 'A' and (resid 62 through 112 )AA62 - 11243 - 93
44chain 'B' and (resid 22 through 44 )BB22 - 441 - 23
55chain 'B' and (resid 45 through 72 )BB45 - 7224 - 51
66chain 'B' and (resid 73 through 100 )BB73 - 10052 - 79
77chain 'B' and (resid 101 through 107 )BB101 - 10780 - 86
88chain 'B' and (resid 108 through 112 )BB108 - 10987 - 88

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