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- PDB-7n9k: KirBac3.1 L124M mutant -

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Basic information

Entry
Database: PDB / ID: 7n9k
TitleKirBac3.1 L124M mutant
ComponentsInward rectifier potassium channel Kirbac3.1
KeywordsMEMBRANE PROTEIN / potassium channel gating / mutant
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding
Similarity search - Function
Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Potassium channel domain / Ion channel / Immunoglobulin E-set
Similarity search - Domain/homology
: / N-OCTANE / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / trimethylamine oxide / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsBlack, T.A. / Gulbis, J.M.
CitationJournal: Nat Commun / Year: 2022
Title: Ion currents through Kir potassium channels are gated by anionic lipids.
Authors: Jin, R. / He, S. / Black, K.A. / Clarke, O.B. / Wu, D. / Bolla, J.R. / Johnson, P. / Periasamy, A. / Wardak, A. / Czabotar, P. / Colman, P.M. / Robinson, C.V. / Laver, D. / Smith, B.J. / Gulbis, J.M.
History
DepositionJun 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Oct 18, 2023Group: 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: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,59313
Polymers33,7691
Non-polymers2,82412
Water72140
1
A: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,37252
Polymers135,0754
Non-polymers11,29848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area33730 Å2
ΔGint-145 kcal/mol
Surface area43100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.577, 106.577, 89.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-506-

K

21A-507-

K

31A-508-

K

41A-509-

K

51A-510-

K

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33768.676 Da / Num. of mol.: 1 / Mutation: C71S, L124M, C262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: D9N164

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#3: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM HEPES pH 7.5, 2.5 w/v % PEG 8K, 2.5% w/v PEG 4K, 20.9% w/w PEG 400, 10% v/v glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.71→47.663 Å / Num. obs: 14347 / % possible obs: 99.8 % / Redundancy: 7.22 % / Biso Wilson estimate: 61.17 Å2 / CC1/2: 1 / Rrim(I) all: 0.17 / Net I/σ(I): 10.52
Reflection shellResolution: 2.71→2.89 Å / Mean I/σ(I) obs: 1.35 / Num. unique obs: 4231 / CC1/2: 0.579 / Rrim(I) all: 1.41 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xl4

1xl4


Resolution: 2.72→42.08 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 700 4.88 %
Rwork0.2175 13642 -
obs0.219 14342 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.24 Å2 / Biso mean: 67.2441 Å2 / Biso min: 26.71 Å2
Refinement stepCycle: final / Resolution: 2.72→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 133 40 2381
Biso mean--80.97 51.56 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.72-2.930.2871410.259326382779
2.93-3.230.28371610.227526562817
3.23-3.690.2221220.210727132835
3.69-4.650.24411360.190127422878
4.65-42.080.2471400.231628933033

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