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- PDB-2wll: POTASSIUM CHANNEL FROM BURKHOLDERIA PSEUDOMALLEI -

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Basic information

Entry
Database: PDB / ID: 2wll
TitlePOTASSIUM CHANNEL FROM BURKHOLDERIA PSEUDOMALLEI
Components(POTASSIUM CHANNEL) x 2
KeywordsMETAL TRANSPORT / TRANSMEMBRANE HELICES / ION CONDUCTION / IMMUNOGLOBULIN FOLD / CYTOSOLIC ASSEMBLY / KIRBAC / K+ CHANNEL / KIR CHANNEL / IONIC CHANNEL / INWARD RECTIFIER / POTASSIUM CHANNEL
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / metal ion 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
: / DIUNDECYL PHOSPHATIDYL CHOLINE / Inward rectifier potassium channel
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.65 Å
AuthorsClarke, O.B. / Caputo, A.T. / Hill, A.P. / VandenBerg, J.I. / Smith, B.J. / Gulbis, J.M.
CitationJournal: Science / Year: 2003
Title: Crystal Structure of the Potassium Channel Kirbac1.1 In the Closed State.
Authors: Kuo, A. / Gulbis, J.M. / Antcliff, J.F. / Rahman, T. / Lowe, E.D. / Zimmer, J. / Cuthbertson, J. / Ashcroft, F.M. / Ezaki, T. / Doyle, D.A.
History
DepositionJun 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references / Other / Refinement description
Revision 1.2Jan 30, 2013Group: Data collection / Database references ...Data collection / Database references / Other / Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Remark 0THIS ENTRY 2WLL REFLECTS A RE-REFINEMENT BY USING PHENIX1.5 AND ANISOTROPICALLY CORRECTED DATA OF ...THIS ENTRY 2WLL REFLECTS A RE-REFINEMENT BY USING PHENIX1.5 AND ANISOTROPICALLY CORRECTED DATA OF THE ORIGINAL STRUCTURAL DATA (R1P7BSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1P7B. PREVIOUSLY DEPOSITED STRUCTURE FACTORS WERE ANISOTROPICALLY SCALED AND ELLIPSOIDALLY TRUNCATED USING THE DIFFRACTION ANISOTROPY SERVER LOCATED AT UCLA. THE ANISOTROPICALLY SCALED FOBS HAVE BEEN DEPOSITED WITH THIS STRUCTURE.: A.KUO,J.M.GULBIS,J.F.ANTCLIFF,T.RAHMAN,E.D.LOWE,J.ZIMMER, J.CUTHBERTSON,F.M.ASHCROFT,T.EZAKI,D.A.DOYLE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POTASSIUM CHANNEL
B: POTASSIUM CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7719
Polymers74,3742
Non-polymers1,3977
Water0
1
A: POTASSIUM CHANNEL
B: POTASSIUM CHANNEL
hetero molecules

A: POTASSIUM CHANNEL
B: POTASSIUM CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,54218
Polymers148,7484
Non-polymers2,79414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area21210 Å2
ΔGint-145 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.840, 105.620, 258.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1310-

MG

21B-1310-

K

31B-1311-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESID 47:309 AND NOT (RESID 196:211 OR RESID 288:301)
211CHAIN B AND RESID 47:309 AND NOT (RESID 196:211 OR RESID 288:301)

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Components

#1: Protein POTASSIUM CHANNEL / / KIRBAC1.1


Mass: 37196.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Gene: CHROMOSOME 1 KIRBAC1.1 / Plasmid: PET-30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: P83698
#2: Protein POTASSIUM CHANNEL / / KIRBAC1.1


Mass: 37177.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Gene: CHROMOSOME 1 KIRBAC1.1 / Plasmid: PET-30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: P83698
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM

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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: 5.58 Å3/Da / Density % sol: 77.77 %
Description: DATA AS PER ENTRY 1P7B, ELLIPSOIDALLY TRUNCATED AND ANISOTROPICALLY SCALED USING DIFFRACTION ANISOTROPY SERVER AT UCLA.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG-400, MAGNESIUM ACETATE, GLYCINE, HEGA-10, PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 3, 2002
RadiationMonochromator: N.A. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.65→20 Å / Num. obs: 14455 / % possible obs: 100 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 95.59 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 4.9
Reflection shellResolution: 3.65→3.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameClassification
RAVEmodel building
SCALAdata scaling
SHELXSphasing
MLPHAREphasing
DMphasing
RAVEphasing
PHENIXrefinement
RefinementMethod to determine structure: MIR / Resolution: 3.65→19.955 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 28.29 / Stereochemistry target values: ML
Details: THE ORIGINAL STRUCTURE FACTORS ARE ASSOCIATED WITH PDB ENTRY 1P7B. THIS ENTRY IS A REREFINEMENT OF PDB ENTRY 1P7B. IMPROVED REFINEMENT STATISTICS WERE OBTAINED.
RfactorNum. reflection% reflection
Rfree0.2857 723 5 %
Rwork0.2463 --
obs0.2482 14447 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.488 Å2 / ksol: 0.248 e/Å3
Displacement parametersBiso mean: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.5385 Å20 Å20 Å2
2--2.5892 Å2-0 Å2
3----2.0507 Å2
Refinement stepCycle: LAST / Resolution: 3.65→19.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 29 0 4043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114170
X-RAY DIFFRACTIONf_angle_d0.9345655
X-RAY DIFFRACTIONf_dihedral_angle_d14.5151387
X-RAY DIFFRACTIONf_chiral_restr0.066635
X-RAY DIFFRACTIONf_plane_restr0.003718
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1771X-RAY DIFFRACTIONPOSITIONAL
12B1771X-RAY DIFFRACTIONPOSITIONAL0.098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6504-3.93030.3211450.29962708X-RAY DIFFRACTION100
3.9303-4.32220.32851450.25642681X-RAY DIFFRACTION100
4.3222-4.93930.25921450.21642733X-RAY DIFFRACTION100
4.9393-6.1920.25961450.2262758X-RAY DIFFRACTION100
6.192-19.9550.2831430.24622844X-RAY DIFFRACTION100
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)
10.3801-1.4009-0.67245.55753.16492.4544-1.1027-4.6650.887-0.8673-2.88892.68080.4278-1.543.97130.3460.76110.07641.4599-0.33131.219247.177721.2836183.9342
23.09870.92941.04294.26414.15197.41610.21180.4399-0.31730.1259-0.0802-0.13181.95241.1158-0.3040.51670.09180.05120.3791-0.15640.164950.343335.6247156.309
30.34990.21-0.10492.3683-1.03570.4579-0.35391.8189-0.1517-1.37590.64460.1270.7480.4794-0.2720.8805-0.0853-0.02461.4777-0.18180.070646.91943.0799152.1197
44.1096-2.15651.652.011-1.43252.2176-0.23980.6821-0.32810.40170.027-0.9519-0.26310.07980.1213-0.12510.4037-0.3321-0.00330.27790.439266.874546.9608198.4543
56.91-1.5262-3.18490.33470.62764.4860.0293-0.1991-0.7939-0.71580.36690.15850.10780.1701-0.37130.4677-0.0759-0.14070.0789-0.04350.632260.067344.84201.9043
62.0768-1.9974-0.64342.8206-1.39073.22260.3250.0189-0.33530.2646-0.04480.53130.48560.4817-0.28590.32620.0973-0.20660.1083-0.01110.316268.641343.897198.4758
76.26296.01337.85658.29686.73351.9991-0.38960.55373.81693.825-2.13783.1232.25490.88832.47620.7721-0.06550.42870.21040.45092.105776.278656.3989184.196
81.7577-0.2111-0.49392.52250.58269.3460.21780.1893-0.0469-0.18040.15860.0494-0.94562.6033-0.12510.3676-0.22460.23770.76460.12840.234163.622856.298156.094
90.9762-0.09640.00253.5353.05112.3450.12810.7461-0.2049-0.70520.04630.1179-0.78840.8997-0.28280.9247-0.12780.14150.7496-0.10610.119555.991853.293152.0467
100.50780.50492.09320.5940.89959.4753-0.1557-0.28280.021-0.10830.71040.2524-1.1749-0.95210.0224-0.3037-0.5117-0.704-0.1744-0.6249-0.01653.010373.6443198.5854
118.9087-0.28821.40130.7768-0.80620.77320.52310.5687-1.26930.5832-0.2349-0.002-0.31620.1348-0.19720.4734-0.1197-0.16190.3498-0.1430.664257.34765.3222202.7938
121.94240.16710.28631.8025-1.97452.16180.07280.2389-0.40660.73270.19610.0415-0.8289-0.3597-0.06230.0552-0.248-0.12420.1793-0.19320.23757.389774.1071198.8477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B AND RESID 27:43)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 44:95)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 96:155)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 156:193)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 194:224)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 225:309)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 38:43)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 44:95)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 96:155)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 156:193)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 194:224)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 225:309)

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