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- PDB-8ayp: NaK C-DI mutant with Rb+ and Ba2+ -

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Basic information

Entry
Database: PDB / ID: 8ayp
TitleNaK C-DI mutant with Rb+ and Ba2+
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
: / RUBIDIUM ION / 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)291198853 Germany
German Research Foundation (DFG)323514590 Germany
German Research Foundation (DFG)446182550 Germany
CitationJournal: J.Chem.Inf.Model. / Year: 2023
Title: Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel.
Authors: Schackert, F.K. / Biedermann, J. / Abdolvand, S. / Minniberger, S. / Song, C. / Plested, A.J.R. / Carloni, P. / Sun, H.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
C: Potassium channel protein
D: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,26141
Polymers42,9434
Non-polymers4,31837
Water1,29772
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)46,67036
Polymers42,9434
Non-polymers3,72732
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area15040 Å2
ΔGint-349 kcal/mol
Surface area15910 Å2
MethodPISA
2
C: Potassium channel protein
D: Potassium channel protein
hetero molecules

C: Potassium channel protein
D: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,85246
Polymers42,9434
Non-polymers4,90942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area19230 Å2
ΔGint-495 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.171, 177.495, 68.042
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-203-

RB

21A-204-

RB

31A-205-

BA

41A-206-

BA

51C-210-

RB

61C-211-

BA

71D-210-

BA

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Components

#1: Protein
Potassium channel protein


Mass: 10735.706 Da / Num. of mol.: 4
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) / References: UniProt: Q81HW2
#2: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-RB / RUBIDIUM ION


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


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.38 Å3/Da / Density % sol: 48.4 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES (NaOH), 40% v/v 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: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.098→44.68 Å / Num. obs: 24497 / % possible obs: 99.37 % / Redundancy: 4.4 % / Biso Wilson estimate: 42.57 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1153 / Rpim(I) all: 0.06133 / Rrim(I) all: 0.1311 / Net I/σ(I): 9.03
Reflection shellResolution: 2.098→2.173 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2383 / CC1/2: 0.393 / CC star: 0.751 / Rpim(I) all: 0.7703 / % possible all: 98.39

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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: 2.1→44.68 Å / SU ML: 0.3047 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 1224 5 %RANDOM
Rwork0.2262 23258 --
obs0.2282 24482 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 240 72 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043113
X-RAY DIFFRACTIONf_angle_d0.66344264
X-RAY DIFFRACTIONf_chiral_restr0.0425538
X-RAY DIFFRACTIONf_plane_restr0.0055478
X-RAY DIFFRACTIONf_dihedral_angle_d8.0046411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.36711330.34282533X-RAY DIFFRACTION98.49
2.18-2.280.37291330.32282531X-RAY DIFFRACTION99.4
2.28-2.40.36381350.30442564X-RAY DIFFRACTION99.85
2.4-2.550.34661340.26392560X-RAY DIFFRACTION99.63
2.55-2.750.25841350.24132561X-RAY DIFFRACTION99.34
2.75-3.030.2891360.22572573X-RAY DIFFRACTION99.74
3.03-3.460.22271370.20752611X-RAY DIFFRACTION99.71
3.46-4.360.22311380.19312614X-RAY DIFFRACTION99.42
4.36-44.680.25981430.21252711X-RAY DIFFRACTION98.89
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)
13.55028930732-0.0770806180094-0.4427049657212.11111421022-0.6172858501534.123577851420.0433984481349-0.259946027570.3880058043820.211675681606-0.0166217571226-0.131366509966-0.251464466773-0.175398891651-0.003501001295730.2435698174960.0386058590790.02152329274340.35513343925-0.07608460869950.331678200627-3.12760001884-22.1822859675-3.983911786
22.943282640150.4947109259950.3673843522511.167024000510.8666475963584.03677541852-0.160568826216-0.05668816283540.441051500595-0.04098550808440.04252479143210.149447192629-0.0815789751244-0.4038700522080.1040349388910.211322096558-4.094302783E-5-0.03058311081110.4130034592690.01614732045310.38950006003-13.1253902265-22.1760357711-19.8245982766
32.76824968914-0.3086296941911.032380382890.7250755490350.3243064461092.916833709190.07740294068050.3312752773470.3151449985530.01640618328890.07464829201380.000263893115178-0.9337571087640.327604078762-0.1593531197670.666197278493-0.189260825920.1405410025230.4123027033540.00687877565440.371650248358-23.0221657958-23.12555775749.72606902613
43.47932018101-0.612783300668-0.4122358450631.23555911315-0.7615808529021.954328023840.04260679485790.2150561929060.382579511410.1074092377060.1905101193780.0728952183857-0.947410724432-0.485015411846-0.07100567176750.6545094751450.2058196676390.09803472489020.4432789880750.1401637444480.388380746733-41.2596191019-23.07119953156.07267145783
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 through 109)AA21 - 1081 - 88
22(chain 'B' and resid 21 through 108)BB21 - 1081 - 88
33(chain 'C' and resid 21 through 113)CC21 - 1131 - 93
44(chain 'D' and resid 21 through 113)DD21 - 1131 - 93

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