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- PDB-2wlk: STRUCTURE OF THE ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL... -

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Basic information

Entry
Database: PDB / ID: 2wlk
TitleSTRUCTURE OF THE ATP-SENSITIVE INWARD RECTIFIER POTASSIUM 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


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
: / SPERMINE / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsClarke, O.B. / Caputo, A.T. / Smith, B.J. / Gulbis, J.M.
CitationJournal: To be Published
Title: Two Intermediate Gating State Crystal Structures of the Kirbac3.1 K+ Channel
Authors: Gulbis, J.M. / Kuo, A. / Smith, B. / Doyle, D.A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M.
History
DepositionJun 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 2WLK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1XL6SF) ...THIS ENTRY 2WLK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1XL6SF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1XL6: J.M.GULBIS,A.KUO,B.SMITH,D.A.DOYLE,A.EDWARDS,C.ARROWSMITH, M.SUNDSTROM
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: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
B: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9999
Polymers67,5662
Non-polymers4337
Water59433
1
A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
B: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)135,99818
Polymers135,1314
Non-polymers86714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area20500 Å2
ΔGint-148.5 kcal/mol
Surface area52890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.760, 107.530, 89.650
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-1302-

K

21A-1303-

K

31A-1304-

K

41A-1305-

K

51A-1307-

K

61B-1302-

SPM

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label alt-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRBTHRAA34 - 13634 - 136
21LEULEUTHRBTHRBB34 - 13634 - 136
12LYSLYSHISHISAA11 - 30111 - 301
22LYSLYSHISHISBB11 - 30111 - 301

NCS ensembles :
ID
1
2

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Components

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


Mass: 33782.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Plasmid: PET-30A / 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.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.77 Å3/Da / Density % sol: 65 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1XL6.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 90MM HEPES, 2.5% PEG 8000, 2.5% PEG 4000, 20% PEG 400, 12.5MM MAGNESIUM CHLORIDE, 42.5MM MAGNESIUM ACETATE, 2.5% GLYCEROL, 14MM HEGA-10 , PH 7.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 28510 / Biso Wilson estimate: 0 Å2

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7B

1p7b


Resolution: 2.8→28.76 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.871 / SU B: 30.591 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REREFINEMENT OF PDB ENTRY 1XL6. IMPROVED REFINEMENT STATISTICS WERE OBTAINED, AND AN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REREFINEMENT OF PDB ENTRY 1XL6. IMPROVED REFINEMENT STATISTICS WERE OBTAINED, AND AN ALTERNATE CONFORMATION OF THE TRANSMEMBRANE DOMAIN WAS MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 1308 5.1 %RANDOM
Rwork0.24668 ---
obs0.24836 24241 99.05 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.034 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--2.68 Å20 Å2
3----4.03 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 20 33 4622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9478462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5355778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.61722.49257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39915929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031536
X-RAY DIFFRACTIONr_chiral_restr0.0830.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214668
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_it2.9671.53888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.36126249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.06232321
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4084.52213
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A770tight positional0.020.05
12B770tight positional0.020.05
21A2249tight positional0.070.05
22B2249tight positional0.070.05
11A770tight thermal1.090.5
12B770tight thermal1.090.5
21A2249tight thermal3.60.5
22B2249tight thermal3.60.5
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.51 77 -
Rwork0.381 1720 -
obs--97.77 %
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)
110.32074.16410.37931.68120.1540.0156-0.51511.2414-0.282-0.20440.5131-0.1134-0.01840.05690.0020.0739-0.0481-0.02160.23190.01220.083545.8151-81.6945212.9958
20.3136-0.01940.83870.11510.13792.5760.0095-0.02670.02220.14-0.08150.020.309-0.16850.07190.2716-0.0185-0.02440.1599-0.03720.048945.7963-64.8813174.8081
30.2705-0.24330.46450.3291-0.7962.25110.02330.0683-0.04270.079-0.08440.0299-0.18840.28360.06110.18370.04250.03610.07510.04040.124261.9817-74.129221.8414
40.0024-0.0834-0.02924.47511.590.57030.10220.0071-0.0255-1.3389-0.66281.3044-0.454-0.24950.56060.48740.2755-0.30360.2268-0.13550.475924.9253-46.8804213.0124
50.34990.3246-0.42150.8191-1.4922.8909-0.0263-0.14510.13810.0640.03970.036-0.1147-0.2844-0.01340.1181-0.0013-0.03930.2739-0.01480.107641.745-46.7359174.5787
60.65720.1693-0.84150.7317-0.17651.3549-0.0115-0.17810.1037-0.19580.0597-0.0530.1180.0295-0.04820.103-0.1070.04970.2421-0.05880.138132.7066-62.8627221.9381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 27
2X-RAY DIFFRACTION2A32 - 136
3X-RAY DIFFRACTION3A137 - 301
4X-RAY DIFFRACTION4B11 - 27
5X-RAY DIFFRACTION5B33 - 136
6X-RAY DIFFRACTION6B137 - 301

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