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- PDB-2x6a: Potassium Channel from Magnetospirillum Magnetotacticum -

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Basic information

Entry
Database: PDB / ID: 2x6a
TitlePotassium Channel from Magnetospirillum Magnetotacticum
ComponentsATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
KeywordsMETAL TRANSPORT / INTEGRAL MEMBRANE PROTEIN / IONIC CHANNEL / ION TRANSPORT / TRANSPORT
Function / homology
Function and homology information


regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / potassium ion import across plasma membrane / monoatomic ion channel complex / identical protein binding / plasma membrane
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
: / PHOSPHOCHOLINE / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsClarke, O.B. / Caputo, A.T. / Hill, A.P. / Vandenberg, J.I. / Smith, B.J. / Gulbis, J.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Domain Reorientation and Rotation of an Intracellular Assembly Regulate Conduction in Kir Potassium Channels.
Authors: Clarke, O.B. / Caputo, A.T. / Hill, A.P. / Vandenberg, J.I. / Smith, B.J. / Gulbis, J.M.
History
DepositionFeb 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0135
Polymers33,7121
Non-polymers3014
Water181
1
A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,05320
Polymers134,8474
Non-polymers1,20616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area18410 Å2
ΔGint-103.2 kcal/mol
Surface area47360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.759, 107.759, 89.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1299-

K

21A-1300-

K

31A-1301-

K

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Components

#1: Protein ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10 / KIRBAC3.1


Mass: 33711.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-320
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HIS-TAG
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: D9N164*PLUS
#2: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625 C-TERMINAL HIS-TAG IN PRESENT ENTRY. ...RESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625 C-TERMINAL HIS-TAG IN PRESENT ENTRY. Q170 HAS BEEN MUTATED TO ALANINE.

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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: 3.84 Å3/Da / Density % sol: 67.98 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROP VAPOUR DIFFUSION, 2:1 PROTEIN:CRYSTALLANT RATIO. CRYSTALLANT: 25% PEG400 2.5% PEG4K 2.5% PEG8K 10% GLYCEROL 90MM HEPES PH 7.5 ADDITIVES: FOS-CHOLINE-ISO-11-6U (ANATRACE) NONYL ...Details: SITTING DROP VAPOUR DIFFUSION, 2:1 PROTEIN:CRYSTALLANT RATIO. CRYSTALLANT: 25% PEG400 2.5% PEG4K 2.5% PEG8K 10% GLYCEROL 90MM HEPES PH 7.5 ADDITIVES: FOS-CHOLINE-ISO-11-6U (ANATRACE) NONYL MALTOSIDE (ANATRACE) FOS-CHOLINE ISO-9 (ANATRACE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0089
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 10032 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 73.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 20.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WLH

2wlh


Resolution: 3.1→44.621 Å / SU ML: 0.47 / σ(F): 0.17 / Phase error: 26.32 / Stereochemistry target values: ML
Details: PHOSPHOCHOLINE BOUND TO CYTOPLASMIC DOMAIN PROBABLY A PARTIALLY DISORDERED FOS-CHOLINE DETERGENT MOLECULE, FOR WHICH WE HAVE MODIFIED THE ZWITTERIONIC HEAD GROUP ONLY.
RfactorNum. reflection% reflection
Rfree0.2713 464 4.8 %
Rwork0.2201 --
obs0.2226 9676 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.595 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6162 Å20 Å2-0 Å2
2--5.6162 Å20 Å2
3----11.2324 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 14 1 2141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142214
X-RAY DIFFRACTIONf_angle_d1.1082984
X-RAY DIFFRACTIONf_dihedral_angle_d22.6311292
X-RAY DIFFRACTIONf_chiral_restr0.071347
X-RAY DIFFRACTIONf_plane_restr0.004375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0998-3.54820.35031500.25022844X-RAY DIFFRACTION92
3.5482-4.46970.25461580.18673080X-RAY DIFFRACTION98
4.4697-44.62560.25531560.2273288X-RAY DIFFRACTION99
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)
11.17750.10060.78180.7933-0.15280.54820.0222-0.6330.03730.5238-0.07620.0862-0.1229-0.6090.04290.46810.09120.16610.6847-0.07250.074843.4768.1344-41.4172
23.26662.1782-3.37514.156-1.47044.3934-0.0483-0.49050.5487-0.21220.01520.73330.01130.49180.04080.60980.0479-0.23830.4056-0.14150.503147.140727.8054-77.9199
31.7126-0.160.23171.1238-0.9351.30480.03820.3716-0.19360.09610.00970.19460.02270.0283-0.05630.0835-0.03560.05380.13170.02280.324664.120619.8638-86.7988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 34:137
2X-RAY DIFFRACTION2CHAIN A AND RESID 12:27
3X-RAY DIFFRACTION3CHAIN A AND RESID 138:301

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