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

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Basic information

Entry
Database: PDB / ID: 2wlh
TitlePOTASSIUM CHANNEL FROM MAGNETOSPIRILLUM MAGNETOTACTICUM
ComponentsPOTASSIUM CHANNEL
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
: / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 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 / Refinement description / 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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0538
Polymers33,7831
Non-polymers2707
Water181
1
A: POTASSIUM CHANNEL
hetero molecules

A: POTASSIUM CHANNEL
hetero molecules

A: POTASSIUM CHANNEL
hetero molecules

A: POTASSIUM CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,21132
Polymers135,1314
Non-polymers1,08028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area24190 Å2
ΔGint-137.1 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.279, 106.279, 90.114
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-1300-

K

21A-1301-

K

31A-1302-

K

41A-1304-

K

51A-1305-

K

61A-1306-

K

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Components

#1: Protein POTASSIUM CHANNEL / KIRBAC3.1


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
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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

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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: 4.24 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: PRECIPITANT: 40 % PEG 200 0.2 M SODIUM CHLORIDE 0.1 M SODIUM PHOSPHATE PH 6.0 PROTEIN: 8MG/ML KB3.1 150MM KCL 20MM TRIS PH 8.0 0.05% TDM 4MM LDAO PROTEIN PRECIPITANT COMBINED IN 1:1 RATIO, ...Details: PRECIPITANT: 40 % PEG 200 0.2 M SODIUM CHLORIDE 0.1 M SODIUM PHOSPHATE PH 6.0 PROTEIN: 8MG/ML KB3.1 150MM KCL 20MM TRIS PH 8.0 0.05% TDM 4MM LDAO PROTEIN PRECIPITANT COMBINED IN 1:1 RATIO, THEN EQUILIBRATED IN SITTING-DROP VAPOUR-DIFFUSION SET-UP WITH RESERVOIR OF PRECIPITANT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956668
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 21, 2008 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956668 Å / Relative weight: 1
ReflectionResolution: 3.28→50 Å / Num. obs: 8448 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.8
Reflection shellResolution: 3.28→3.4 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % possible all: 90.4

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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: 3.28→15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.859 / SU B: 44.264 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-11, 28-32 AND 300-301 ARE DISORDERED. STRUCTURE WAS INITIALLY REFINED IN PHENIX, THEN TRANSFERRED TO REFMAC FOR FINAL REFINEMENT. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-11, 28-32 AND 300-301 ARE DISORDERED. STRUCTURE WAS INITIALLY REFINED IN PHENIX, THEN TRANSFERRED TO REFMAC FOR FINAL REFINEMENT. ANISOTROPIC THERMAL PARAMETERS WERE INTRODUCED USING TLS IN PHENIX, NOT REFINED EXPLICITLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 497 6.16 %SHELLS
Rwork0.2128 ---
obs0.216 8140 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 95.905 Å2
Baniso -1Baniso -2Baniso -3
1-2.605 Å20 Å20 Å2
2--2.605 Å20 Å2
3----5.21 Å2
Refinement stepCycle: LAST / Resolution: 3.28→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 7 1 2234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9373104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5415281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15522.33103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15115358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0251517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211727
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.2641.51405
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.87122268
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.293878
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9474.5836
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: 3.279→3.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.284 556 -
Rfree-0 -
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)
11.254-0.96921.28811.53850.12942.92810.1825-0.0001-0.0379-0.4805-0.36130.1713-0.2666-0.49340.17880.18110.149-0.00370.16-0.01530.502-9.833-31.94718.741
20.20750.1336-0.08990.1635-0.53923.1267-0.1574-0.0718-0.2336-0.0094-0.0259-0.1608-0.4791-0.30690.18320.1960.11570.14470.21480.03650.2735-11.541-40.18146.291
36.3910.62933.319711.21427.49936.33890.3635-0.5234-0.1354-0.5014-0.36980.1116-0.171-0.49680.00630.21090.06320.10280.31490.0160.096-14.747-45.40467.494
45.1723-0.483-0.30710.04770.10312.3945-0.1037-0.326-0.16880.00740.03490.0179-0.0792-0.16660.06880.26510.0740.06640.1655-0.02690.1237-8.317-44.63757.987
53.773-1.5192-3.2594.35022.22553.0410.21390.62710.31340.31380.0417-0.0204-0.0768-0.4923-0.25560.1335-0.01820.02140.32720.09640.1464-13.562-53.49757.636
67.4121.4774-5.07634.8026-1.67913.5821-0.4115-0.1197-0.32280.05180.0826-0.54290.2760.03290.32890.1764-0.04230.01620.1856-0.15540.2714-2.845-46.43934.275
70.72440.41380.26691.0503-1.08314.1321-0.01020.07980.0084-0.0417-0.01820.1271-0.10720.24550.02850.1657-0.02450.0290.12260.00920.19239.186-33.4922.13
88.71746.58069.104613.38076.82049.5145-0.1623-0.3698-0.2678-0.29440.43670.4717-0.1855-0.3725-0.27440.18980.0606-0.08810.24650.05520.1348-14.588-28.877-7.526
926.95844.137915.79814.6946.411713.18460.09450.9802-1.1459-0.48480.3906-0.0818-0.41260.8039-0.48510.465-0.0380.01060.35270.16950.777732.486-36.899.226
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

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