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- PDB-7oou: NaK C-DI mutant with Li+ and K+ -

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Basic information

Entry
Database: PDB / ID: 7oou
TitleNaK C-DI mutant with Li+ and K+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium channel activity / membrane / metal ion binding / identical protein binding
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: 1.8 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
DepositionMay 28, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,70730
Polymers21,4712
Non-polymers2,23628
Water97354
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)47,41460
Polymers42,9434
Non-polymers4,47256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area18650 Å2
ΔGint-357 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.481, 88.413, 49.586
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-202-

K

31A-203-

K

41A-204-

K

51B-207-

ACT

61B-207-

ACT

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Components

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Protein , 1 types, 2 molecules AB

#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 (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 , 6 types, 82 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / 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.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.07 Å3/Da / Density % sol: 40.5 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM K acetate, 40% 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: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→44.21 Å / Num. obs: 16950 / % possible obs: 99.71 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.93 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1172 / Rpim(I) all: 0.04918 / Rrim(I) all: 0.1272 / Net I/σ(I): 12.46
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.99 / Num. unique obs: 1671 / CC1/2: 0.398 / CC star: 0.754 / Rpim(I) all: 0.789 / % possible all: 99.76

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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: 1.8→44.21 Å / SU ML: 0.2578 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 850 5 %
Rwork0.1764 16145 -
obs0.1779 16941 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 142 54 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561624
X-RAY DIFFRACTIONf_angle_d0.76062210
X-RAY DIFFRACTIONf_chiral_restr0.044273
X-RAY DIFFRACTIONf_plane_restr0.0044259
X-RAY DIFFRACTIONf_dihedral_angle_d7.7913210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.910.38351370.35642603X-RAY DIFFRACTION97.34
1.91-2.060.25021400.21562656X-RAY DIFFRACTION99.79
2.06-2.260.21181400.17852673X-RAY DIFFRACTION99.82
2.26-2.590.19021420.14282687X-RAY DIFFRACTION99.72
2.59-3.260.18891420.15452706X-RAY DIFFRACTION99.89
3.26-44.210.19241490.17362820X-RAY DIFFRACTION99.43
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)
12.13015564672-0.757936147688-0.05798704428181.147798801371.224817351262.14375074765-0.06277653416260.01060431733760.131979475787-0.1066080462290.101335740167-0.432571680683-0.1909329697110.051059347835-0.0007558413286020.1577909677920.00369469939649-0.03096706476630.215946263684-0.03160639870650.19531844901918.137840424425.3259147533-4.7788784153
20.428365480821-0.250860066187-0.2135358830790.187469471947-0.08498191974831.02154548449-0.00604318179731-0.0937384820931-0.474693456568-0.1031638824530.008990613815470.3111603091160.375981297239-0.2121912874860.001298966925260.247598750077-0.00779450854581-0.004652291991670.1927259154920.01588883105610.25278464939310.133714090912.3578150001-7.14043468051
30.965555441553-0.468013266034-0.2329938763120.550199117530.4772524349291.01228972790.08455411740920.07125055471270.05653694937880.211341002788-0.0643833074911-0.0644087201623-0.55605947035-0.0832013967659-3.18936954321E-50.191082193130.00276382039466-0.01286729131490.215611379755-0.0005990069855670.189942642810.066143007727.3544573868-9.35841626503
41.82916084170.8906622706780.08947481032550.5632528504720.5727524262472.169291143760.1096246348190.2747308455970.491935646-0.487334153069-0.120129382058-0.113843371116-0.40282847007-0.00736558642350.001118818179380.2515303128160.0007076090921830.03031107301680.2490382760050.02916613213070.2102899840658.5771802725225.5777384715-29.8749623658
52.680510571370.1545858659230.5339203820690.3801698817470.04615240404271.674324585380.00962424845159-0.0503724881017-0.003009955936690.0174426764447-0.01800022622390.0933439655890.034913242971-0.04660635582696.64835741462E-50.177631889685-0.006148478742210.01089189827020.177302227535-0.00511168333670.1713246419886.5539670128119.0510140091-21.618734237
60.2096238822540.127597107791-0.1259156243760.1981400142330.123712118930.407804586188-0.01963620167140.5568281705990.0665925805995-0.144521129907-0.0915203821161-0.008169420225420.1880113780740.0953431613597-0.0001691042642490.2845547299140.0245091614974-0.04516348760410.2503931629230.007133811533050.33440597-15.768878617338.8227999574-28.8790123466
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 45 )AA20 - 451 - 26
22chain 'A' and (resid 46 through 72 )AA46 - 7227 - 53
33chain 'A' and (resid 73 through 108 )AA73 - 10854 - 89
44chain 'B' and (resid 20 through 45 )BB20 - 451 - 26
55chain 'B' and (resid 46 through 100 )BB46 - 10027 - 81
66chain 'B' and (resid 101 through 113 )BB101 - 11382 - 94

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