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- PDB-2wli: POTASSIUM CHANNEL FROM MAGNETOSPIRILLUM MAGNETOTACTICUM -

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Basic information

Entry
Database: PDB / ID: 2wli
TitlePOTASSIUM CHANNEL FROM MAGNETOSPIRILLUM MAGNETOTACTICUM
Components
  • KIRBAC3.1 POTASSIUM CHANNEL
  • POTASSIUM CHANNEL
KeywordsMETAL TRANSPORT / INTEGRAL MEMBRANE PROTEIN / IONIC CHANNEL / ION TRANSPORT / TRANSPORT
Function / homology
Function and homology information


inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / 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
: / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsClarke, O.B. / Caputo, A.T. / 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
DepositionJun 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 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_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_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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POTASSIUM CHANNEL
B: KIRBAC3.1 POTASSIUM CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7666
Polymers67,6102
Non-polymers1564
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-33 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.409, 105.009, 89.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1300-

K

21A-1301-

K

31A-1302-

K

41A-1303-

K

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Components

#1: Protein POTASSIUM CHANNEL / KIRBAC3.1


Mass: 33826.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Description: EXPRESSED RECOMBINANTLY IN ESCHERICHIA COLI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: D9N164*PLUS
#2: Protein KIRBAC3.1 POTASSIUM CHANNEL


Mass: 33782.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Description: EXPRESSED RECOMBINANTLY IN ESCHERICHIA COLI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: D9N164*PLUS
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625, CHAIN A INCLUDES LEU200ARG CONFLICT.

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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: 4.44 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PRECIPITANT: 15 % PEG 400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN: 8MG/ML KIRBAC3.1 150MM KCL 20MM TRIS8.0 0.05% TDM 4MM LDAO PROTEIN AND PRECIPITANT WERE ...Details: PRECIPITANT: 15 % PEG 400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN: 8MG/ML KIRBAC3.1 150MM KCL 20MM TRIS8.0 0.05% TDM 4MM LDAO PROTEIN AND PRECIPITANT WERE COMBINED IN A 1:1 RATIO AND EQUILIBRATED AGAINST A RESERVOIR OF PRECIPITANT IN A SITTING-DROP VAPOUR-DIFFUSION SET-UP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953639
DetectorType: ADSC CCD / Detector: CCD / Date: May 18, 2008 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953639 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 20089 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XL4

1xl4


Resolution: 3.09→15 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.841 / SU B: 47.031 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R: 1.322 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28767 998 5 %SHELLS
Rwork0.26538 ---
obs0.26655 18847 100 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.917 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å20 Å2
2--1.02 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 3.09→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 4 2 4267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214395
X-RAY DIFFRACTIONr_bond_other_d00.024010
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9325989
X-RAY DIFFRACTIONr_angle_other_deg3.09839213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.64122.165194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34915667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0961530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024905
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02979
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.52719
X-RAY DIFFRACTIONr_mcbond_other01.51114
X-RAY DIFFRACTIONr_mcangle_it024382
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it031676
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it04.51604
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.094→3.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.335 1309 -
obs--100 %
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)
10.2848-0.45031.00351.6449-1.16174.31910.0572-0.0126-0.08810.2461-0.12690.24940.4939-0.00710.06970.1655-0.02570.09230.11890.00830.2444-22.539-60.610417.4741
20.4023-0.147-0.41240.41990.60061.03190.07430.041-0.01260.181-0.10540.09770.2265-0.0770.03110.2084-0.045-0.06530.2717-0.04230.2165-14.0652-62.981845.4444
33.9432-0.6443-6.2248.56244.082510.9359-0.1671-0.1395-0.19290.96240.0045-0.33960.60650.20510.16260.1777-0.117-0.05760.26940.0420.1107-9.126-66.83566.6736
41.80451.6833-1.18331.8528-1.33140.9608-0.30830.35740.1491-0.16260.41840.16410.1131-0.3071-0.11010.2068-0.0610.02040.18330.02180.0731-9.2159-60.158657.1848
51.38410.32710.14120.2541.11926.81910.00090.0341-0.1190.0260.0333-0.01630.13970.1532-0.03420.0837-0.01310.00840.01940.00670.0785-0.7542-66.05857.6317
63.05271.5133-0.61693.9615-5.0097.73320.50220.23570.036-0.2058-0.2320.30340.48020.2457-0.27020.15690.1133-0.05260.123-0.07530.0593-7.0102-55.138334.0923
72.5508-0.57661.02562.30810.49564.5753-0.02760.19630.0468-0.1476-0.02160.0259-0.23450.02690.04920.0187-0.0011-0.00380.01630.00380.0018-19.5964-41.62582.1489
80.4815-0.6126-0.94685.93982.64323.4475-0.016-0.0416-0.0280.246-0.06140.0930.18810.01340.07740.0264-0.02760.00320.0637-0.00870.0323-25.5251-65.0108-7.6387
91.6747-0.93282.1139.4976-2.01632.74590.13790.0135-0.24680.26640.17370.01710.13050.0034-0.31160.1320.01240.05060.0453-0.03160.1739-17.9627-19.06369.6404
103.7329-1.75270.21577.6683-4.38292.7586-0.2660.24980.138-0.41740.32250.05930.19-0.3655-0.05660.34660.1042-0.01610.2765-0.08880.1871-13.3885-33.590223.5001
110.43470.03670.29431.9472-0.50521.5659-0.1472-0.08140.2291-0.1760.28870.08690.2771-0.2907-0.14150.28590.0036-0.08540.11460.01520.2298-10.5499-38.360345.4714
124.74380.90422.03981.17642.49845.30940.1581-0.1047-0.0976-0.00070.0048-0.07490.00160.0078-0.16290.04440.01350.02260.04970.00460.0385-14.3151-43.429766.6976
133.0011-4.4576-0.42856.63920.56860.56080.0540.1138-0.1125-0.0077-0.16910.1825-0.3811-0.15560.11510.32590.0617-0.01040.143-0.05230.1477-7.6639-43.268157.1893
141.7831.4306-0.40632.3353-0.52346.51330.0318-0.15570.1380.2469-0.16440.29460.2646-0.35520.13260.07210.01310.05530.1993-0.03350.0697-13.5472-51.748657.6109
153.3636-1.004-3.57154.5476-0.22587.2579-0.7075-0.21870.3085-0.21590.4675-0.4880.3409-0.11670.240.28780.0511-0.09880.0868-0.07670.1416-2.9183-45.597734.351
161.87910.2884-0.53072.5332-1.49085.3186-0.04950.00710.1032-0.01930.06450.2731-0.2967-0.0843-0.0150.02580.0022-0.01230.00250.00360.045411.0791-33.78172.1259
179.5551-1.3917-6.433610.0205-8.700113.792-0.90180.49350.3068-0.0183-0.3565-1.52470.7504-0.05451.25830.4286-0.0618-0.0480.45160.08230.5569-6.7296-25.0071-2.7324
1810.296-2.9277-1.80760.90460.65330.58720.0852-0.23120.15720.02090.1168-0.13830.07550.1421-0.2020.06340.0108-0.04680.1118-0.02020.176533.3846-38.98968.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 43
2X-RAY DIFFRACTION2A44 - 71
3X-RAY DIFFRACTION3A72 - 81
4X-RAY DIFFRACTION4A82 - 100
5X-RAY DIFFRACTION5A101 - 120
6X-RAY DIFFRACTION6A121 - 137
7X-RAY DIFFRACTION7A138 - 182
8X-RAY DIFFRACTION7A194 - 274
9X-RAY DIFFRACTION7A286 - 299
10X-RAY DIFFRACTION8A183 - 193
11X-RAY DIFFRACTION9A275 - 285
12X-RAY DIFFRACTION10B12 - 43
13X-RAY DIFFRACTION11B44 - 71
14X-RAY DIFFRACTION12B72 - 81
15X-RAY DIFFRACTION13B82 - 100
16X-RAY DIFFRACTION14B101 - 120
17X-RAY DIFFRACTION15B121 - 137
18X-RAY DIFFRACTION16B138 - 182
19X-RAY DIFFRACTION16B194 - 274
20X-RAY DIFFRACTION16B286 - 299
21X-RAY DIFFRACTION17B183 - 193
22X-RAY DIFFRACTION18B275 - 285

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