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- PDB-7oph: NaK S-DI mutant with Na+ and K+ -

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Basic information

Entry
Database: PDB / ID: 7oph
TitleNaK S-DI mutant with Na+ and K+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN
Function / homologyTwo pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / identical protein binding / membrane / metal ion binding / : / Potassium channel protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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., Sect. 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
DepositionMay 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 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)23,75427
Polymers21,4392
Non-polymers2,31425
Water1,45981
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)47,50754
Polymers42,8794
Non-polymers4,62950
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)81.130, 88.021, 49.313
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-201-

K

21A-203-

K

31B-201-

K

41B-333-

HOH

51B-338-

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, 106 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.04 Å3/Da / Density % sol: 39.7 % / 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.42→38.01 Å / Num. obs: 33665 / % possible obs: 99.76 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.55 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08316 / Rpim(I) all: 0.03565 / Rrim(I) all: 0.09065 / Net I/σ(I): 12.67
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 3308 / CC1/2: 0.403 / CC star: 0.758 / % possible all: 99.61

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+86 / Resolution: 1.42→38.01 Å / SU ML: 0.218 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1794 1683 4.99 %
Rwork0.1528 32014 -
obs0.1542 33624 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.98 Å2
Refinement stepCycle: LAST / Resolution: 1.42→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 144 81 1678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721674
X-RAY DIFFRACTIONf_angle_d0.90182305
X-RAY DIFFRACTIONf_chiral_restr0.0639288
X-RAY DIFFRACTIONf_plane_restr0.005262
X-RAY DIFFRACTIONf_dihedral_angle_d12.9655555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.37271360.34422601X-RAY DIFFRACTION97.65
1.46-1.510.35251370.28092611X-RAY DIFFRACTION99.64
1.51-1.560.29451390.26932637X-RAY DIFFRACTION99.61
1.56-1.620.35281380.2442644X-RAY DIFFRACTION99.68
1.62-1.70.29031400.20382642X-RAY DIFFRACTION99.71
1.7-1.790.20711380.16392634X-RAY DIFFRACTION99.86
1.79-1.90.20861410.14752681X-RAY DIFFRACTION99.93
1.9-2.050.18471400.12212658X-RAY DIFFRACTION99.93
2.05-2.250.14821410.10452677X-RAY DIFFRACTION99.96
2.25-2.580.13891420.11152697X-RAY DIFFRACTION99.96
2.58-3.250.13371430.13142707X-RAY DIFFRACTION99.82
3.25-38.010.17551480.16612825X-RAY DIFFRACTION99.6

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