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- PDB-6o9u: KirBac3.1 at a resolution of 2 Angstroms -

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Basic information

Entry
Database: PDB / ID: 6o9u
TitleKirBac3.1 at a resolution of 2 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
: / : / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / trimethylamine oxide / 3,3',3''-phosphoryltripropanoic acid / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGulbis, J.M. / Clarke, O.B.
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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37318
Polymers33,7831
Non-polymers2,59017
Water3,009167
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)145,49372
Polymers135,1314
Non-polymers10,36268
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 area31740 Å2
ΔGint-243 kcal/mol
Surface area43210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.955, 105.955, 89.639
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-404-

K

21A-405-

K

31A-406-

K

41A-407-

K

51A-408-

K

61A-409-

K

71A-410-

K

81A-413-

BA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33782.766 Da / Num. of mol.: 1
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 , 7 types, 184 molecules

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


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


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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.: 2 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#7: Chemical ChemComp-Z3P / 3,3',3''-phosphoryltripropanoic acid


Mass: 266.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O7P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.5% PEG 4k, 2.5% PEG 8k, 10-17% PEG 400, 90 mM HEPES pH 7.5, 1 mM TCEP, and 50 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.61 Å / Num. obs: 65702 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.97
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.24 / Num. unique obs: 6508 / % possible all: 100

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Processing

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

1xl4


Resolution: 2→45.608 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2271 3311 5.04 %
Rwork0.2021 --
obs0.2034 65702 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.46 Å2 / Biso mean: 43.0896 Å2 / Biso min: 22.1 Å2
Refinement stepCycle: final / Resolution: 2→45.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 121 168 2504
Biso mean--57.44 45.36 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032348
X-RAY DIFFRACTIONf_angle_d0.5453197
X-RAY DIFFRACTIONf_chiral_restr0.044361
X-RAY DIFFRACTIONf_plane_restr0.003403
X-RAY DIFFRACTIONf_dihedral_angle_d11.2751359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.02880.31971370.33172542267999
2.0288-2.05910.3151280.310425962724100
2.0591-2.09130.32381400.30526072747100
2.0913-2.12560.30461450.286726112756100
2.1256-2.16220.29021150.286626232738100
2.1622-2.20150.2681470.26725982745100
2.2015-2.24390.2681370.26525922729100
2.2439-2.28970.25881260.246825902716100
2.2897-2.33950.26121400.243726322772100
2.3395-2.39390.26091720.227925792751100
2.3939-2.45370.23231340.220925992733100
2.4537-2.52010.21931530.211625742727100
2.5201-2.59420.24851520.198825832735100
2.5942-2.6780.25321540.191325892743100
2.678-2.77370.22971390.19226452784100
2.7737-2.88470.24091340.18926042738100
2.8847-3.0160.20881490.171226002749100
3.016-3.17490.21521660.170825482714100
3.1749-3.37380.2211220.167226172739100
3.3738-3.63420.20641080.166626482756100
3.6342-3.99970.18381310.174525942725100
3.9997-4.5780.22941310.1692602273399
4.578-5.7660.19491350.188826222757100
5.766-45.61960.20991160.22972596271299

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