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- PDB-6o9t: KirBac3.1 mutant at a resolution of 4.1 Angstroms -

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Basic information

Entry
Database: PDB / ID: 6o9t
TitleKirBac3.1 mutant at a resolution of 4.1 Angstroms
ComponentsInward rectifier potassium channel Kirbac3.1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / identical protein binding / plasma membrane
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
Chem-6E3 / : / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,0634
Polymers33,7931
Non-polymers2703
Water00
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)136,25316
Polymers135,1714
Non-polymers1,08212
Water0
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 area17030 Å2
ΔGint-144 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.110, 103.110, 89.270
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-401-

K

21A-402-

K

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Components

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33792.785 Da / Num. of mol.: 1 / Mutation: C71V, C119V, C262S, A133C, T136C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: D9N164
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-6E3 / 2,3,5,6-tetramethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2 / Feature type: SUBJECT OF INVESTIGATION

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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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 33% (v/v) PEG 400, 0.1 M MES, pH 6.5; 4% (v/v) ethylene glycol, 0.1 M NaCl

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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: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.9→46.11 Å / Num. obs: 4688 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.999 / Rrim(I) all: 0.168 / Net I/σ(I): 7.74
Reflection shellResolution: 3.9→4.14 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 702 / CC1/2: 0.33 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XL4

1xl4


Resolution: 4.01→46.11 Å / Cor.coef. Fo:Fc: 0.8761 / Cor.coef. Fo:Fc free: 0.9283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.759
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 195 4.49 %RANDOM
Rwork0.246 ---
obs0.2472 4340 99.56 %-
Displacement parametersBiso max: 280.17 Å2 / Biso mean: 219.28 Å2 / Biso min: 140.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.2824 Å20 Å20 Å2
2---4.2824 Å20 Å2
3---8.5648 Å2
Refine analyzeLuzzati coordinate error obs: 1.179 Å
Refinement stepCycle: final / Resolution: 4.01→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 16 0 2071
Biso mean--223.25 --
Num. residues----274
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d661SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes343HARMONIC5
X-RAY DIFFRACTIONt_it2124HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2387SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2124HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2907HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion22.7
LS refinement shellResolution: 4.01→4.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2571 52 4.34 %
Rwork0.2519 1147 -
all0.2521 1199 -
obs--99.56 %
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)
19.6819-6.7486-5.006710.75861.85672.23340.05370.03210.0818-0.03680.01590.1359-0.6243-0.0775-0.0696-0.60250.387-0.2268-0.102-0.18210.826-11.1923-23.5736.6611
26.60621.27591.95033.3799-0.692513.8738-0.0622-1.82020.94791.22690.12431.06010.0545-1.218-0.0620.62180.26180.29040.3856-0.3811-0.547-9.2904-41.955347.2484
321.9316-7.22268.43018.1776-1.41177.73880.38370.881.4039-0.5737-0.7319-0.57060.75810.3690.3482-0.4013-0.03090.20120.07910.38960.31565.4702-31.2040.5893
40.26540.1696-0.08350.4231-0.08350.2575-0.00390.01050.0051-0.00320.0036-0.0132-0.0234-0.00940.00030.3232-0.3515-0.03760.38530.25260.09766.8566-44.812924.8819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|8 - A|26 }A8 - 26
2X-RAY DIFFRACTION2{ A|35 - A|136 }A35 - 136
3X-RAY DIFFRACTION3{ A|137 - A|295 }A137 - 295
4X-RAY DIFFRACTION4{ A|403 - A|403 }A403

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