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- PDB-6o9v: KirBac3.1 mutant at a resolution of 3.1 Angstroms -

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Basic information

Entry
Database: PDB / ID: 6o9v
TitleKirBac3.1 mutant at a resolution of 3.1 Angstroms
ComponentsInward rectifier potassium channel Kirbac3.1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding
Similarity search - Function
G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulin E-set ...G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DECYLAMINE-N,N-DIMETHYL-N-OXIDE / : / 1,1-Methanediyl Bismethanethiosulfonate / trimethylamine oxide / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.094 Å
AuthorsGulbis, J.M. / Black, K.A. / Miller, D.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2020
Title: A constricted opening in Kir channels does not impede potassium conduction.
Authors: Black, K.A. / He, S. / Jin, R. / Miller, D.M. / Bolla, J.R. / Clarke, O.B. / Johnson, P. / Windley, M. / Burns, C.J. / Hill, A.P. / Laver, D. / Robinson, C.V. / Smith, B.J. / Gulbis, J.M.
History
DepositionMar 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inward rectifier potassium channel Kirbac3.1
B: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,60411
Polymers67,4612
Non-polymers1,1439
Water37821
1
A: Inward rectifier potassium channel Kirbac3.1
B: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
B: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,20922
Polymers134,9234
Non-polymers2,28618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area21220 Å2
ΔGint-120 kcal/mol
Surface area47680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.298, 114.683, 89.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-402-

K

21A-403-

K

31A-404-

K

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33730.715 Da / Num. of mol.: 2 / Mutation: C71V, C119V, S129C, F135C, C262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: D9N164

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Non-polymers , 5 types, 30 molecules

#2: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#5: Chemical ChemComp-M1M / 1,1-Methanediyl Bismethanethiosulfonate / S,S'-methylene dimethanesulfonothioate


Mass: 236.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O4S4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 13% (w/v) PEG MME 2000, 0.1 M TRIS HCl, pH 7.1, 0.1 M CaCl2 and 1% (w/v) LDAO

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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: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→48.27 Å / Num. obs: 17691 / % possible obs: 99 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.22 / Net I/σ(I): 12.6
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2785 / CC1/2: 0.47 / Rrim(I) all: 2.17

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XL4

1xl4


Resolution: 3.094→44.728 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.62
RfactorNum. reflection% reflection
Rfree0.2936 835 5.21 %
Rwork0.248 --
obs0.2503 16018 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.11 Å2 / Biso mean: 92.4515 Å2 / Biso min: 38.95 Å2
Refinement stepCycle: final / Resolution: 3.094→44.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 48 21 4420
Biso mean--87.7 73.81 -
Num. residues----561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034501
X-RAY DIFFRACTIONf_angle_d0.7066132
X-RAY DIFFRACTIONf_chiral_restr0.04710
X-RAY DIFFRACTIONf_plane_restr0.003771
X-RAY DIFFRACTIONf_dihedral_angle_d10.5392605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0944-3.28820.38661400.336224562596
3.2882-3.5420.36041350.288524802615
3.542-3.89820.30791530.257724822635
3.8982-4.46190.31511290.222125282657
4.4619-5.61980.24221290.218925762705
5.6198-44.73320.2731490.250426612810

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