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- PDB-8a7x: NaK C-DI F92A mutant soaked in Cs+ -

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Basic information

Entry
Database: PDB / ID: 8a7x
TitleNaK C-DI F92A mutant soaked in Cs+
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 / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 21, 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)24,17329
Polymers21,3192
Non-polymers2,85427
Water50428
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)47,10452
Polymers42,6384
Non-polymers4,46648
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 area21610 Å2
ΔGint-822 kcal/mol
Surface area14460 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)49,58964
Polymers42,6384
Non-polymers6,95160
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 area21030 Å2
ΔGint-780 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.160, 68.160, 90.250
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-

CS

21A-209-

K

31A-210-

K

41A-211-

K

51B-201-

CS

61B-202-

CS

71B-203-

CS

81B-215-

K

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Components

#1: Protein Potassium channel protein


Mass: 10659.609 Da / Num. of mol.: 2 / Mutation: D66C G67- N68D F69I F92A
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-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.46 Å3/Da / Density % sol: 49.97 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200 mM CsCl 100 mM Tris-HCl pH 8.0, 63% MPD (2-Methyl-2,4-pentanediol racemate) - soaked in 90 mM CsCl, 100 mM Kryptofix-222, 50% MPD

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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: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→45.12 Å / Num. obs: 22957 / % possible obs: 96.07 % / Redundancy: 2.2 % / Biso Wilson estimate: 44.36 Å2 / CC1/2: 0.936 / CC star: 0.983 / Rmerge(I) obs: 0.1228 / Rpim(I) all: 0.09434 / Net I/σ(I): 44.22
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.9152 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2360 / CC1/2: 0.392 / CC star: 0.75 / Rpim(I) all: 0.7146 / % possible all: 96.97

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+86 / Resolution: 2.1→45.12 Å / SU ML: 0.3202 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2401 1139 4.99 %
Rwork0.1969 21709 -
obs0.1991 22848 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 153 28 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01441610
X-RAY DIFFRACTIONf_angle_d1.42732207
X-RAY DIFFRACTIONf_chiral_restr0.0716280
X-RAY DIFFRACTIONf_plane_restr0.0094244
X-RAY DIFFRACTIONf_dihedral_angle_d15.2503214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.39961440.32572808X-RAY DIFFRACTION97.04
2.2-2.310.36341350.30922525X-RAY DIFFRACTION91.28
2.31-2.460.28781450.25822719X-RAY DIFFRACTION95.47
2.46-2.640.21691450.21272763X-RAY DIFFRACTION98.24
2.65-2.910.28091440.22572730X-RAY DIFFRACTION97.46
2.91-3.330.26441410.19552707X-RAY DIFFRACTION95.16
3.33-4.190.23921440.17892743X-RAY DIFFRACTION98.03
4.21-45.120.18711410.16492714X-RAY DIFFRACTION95.93

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