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- PDB-7n9l: KirBac3.1 C71S C262S -

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Basic information

Entry
Database: PDB / ID: 7n9l
TitleKirBac3.1 C71S C262S
ComponentsInward rectifier potassium channel Kirbac3.1
KeywordsMEMBRANE PROTEIN / Potassium channel
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
: / 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: 2.4 Å
AuthorsGulbis, J.M. / Black, K.A.
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)37,32615
Polymers33,7511
Non-polymers3,57514
Water1,56787
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)149,30460
Polymers135,0034
Non-polymers14,30256
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 area27120 Å2
ΔGint-187 kcal/mol
Surface area46980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.884, 106.884, 89.760
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-406-

K

21A-408-

K

31A-409-

K

41A-410-

K

51A-411-

K

61A-412-

K

71A-413-

K

81A-415-

K

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Components

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33750.637 Da / Num. of mol.: 1 / Mutation: C71S, 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
#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.: 4 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#3: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 3.8 Å3/Da / Density % sol: 67.61 %
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: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→47.8 Å / Num. obs: 20993 / % possible obs: 99.8 % / Redundancy: 13.16 % / Biso Wilson estimate: 50.21 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.245 / Net I/σ(I): 8.6
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 11.84 % / Mean I/σ(I) obs: 0.52 / Num. unique obs: 3316 / CC1/2: 0.404 / Rrim(I) all: 2.534 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å47.8 Å
Translation4 Å47.8 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xl4

1xl4


Resolution: 2.4→47.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1050 5.01 %
Rwork0.2278 19900 -
obs0.2293 20950 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.2 Å2 / Biso mean: 60.83 Å2 / Biso min: 29.65 Å2
Refinement stepCycle: final / Resolution: 2.4→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 103 87 2406
Biso mean--70.93 56.36 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.510.3561310.32322407253899
2.51-2.640.33241470.267224282575100
2.64-2.80.2731320.263524432575100
2.8-3.020.30091350.240524502585100
3.02-3.320.26371360.212824742610100
3.33-3.810.24911110.201724982609100
3.81-4.790.21631300.189125182648100
4.8-47.80.25181280.2526822810100

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