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

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Basic information

Entry
Database: PDB / ID: 2wlo
TitlePOTASSIUM CHANNEL FROM MAGNETOSPIRILLUM MAGNETOTACTICUM
ComponentsPOTASSIUM CHANNEL
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN
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
Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Potassium channel domain / Ion channel / Immunoglobulin E-set
Similarity search - Domain/homology
: / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 4.036 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 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2Apr 17, 2013Group: Source and taxonomy
Revision 1.3May 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 1.4Sep 4, 2019Group: Data collection / Category: reflns
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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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)67,6835
Polymers67,5662
Non-polymers1173
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-36.8 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.860, 115.360, 289.110
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-1300-

K

21A-1301-

K

31A-1302-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 137:184 OR RESSEQ 193:275 OR RESSEQ 285:295 )
211CHAIN B AND (RESSEQ 137:184 OR RESSEQ 193:275 OR RESSEQ 285:295 )
112CHAIN A AND (RESSEQ 34:136 )
212CHAIN B AND (RESSEQ 34:136 )

NCS ensembles :
ID
1
2

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Components

#1: Protein POTASSIUM CHANNEL / KIRBAC3.1


Mass: 33782.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: D9N164*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K

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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: 7.36 Å3/Da / Density % sol: 83 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PRECIPITANT: 15 % PEG400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN KIRBAC 3.1, 8MG/ML 150MM KCL 20MM TRIS PH 8.0 20MM TETRABUTYL AMMONIUM BROMIDE 4MM CYMAL-5 0. ...Details: PRECIPITANT: 15 % PEG400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN KIRBAC 3.1, 8MG/ML 150MM KCL 20MM TRIS PH 8.0 20MM TETRABUTYL AMMONIUM BROMIDE 4MM CYMAL-5 0.05% TDM PROTEIN AND PRECIPITANT WERE MIXED TOGETHER IN A 1:1 RATIO, AND EQUILIBRATED AGAINST RESERVOIR SOLUTION 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: 0.957
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2008 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 0 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 136.35 Å2 / Rmerge(I) obs: 0.224 / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 4.036→14.995 Å / SU ML: -0 / σ(F): 1.47 / Phase error: 25.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2547 663 4.9 %
Rwork0.2447 --
obs0.2453 13507 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 126.749 Å2 / ksol: 0.285 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--53.7271 Å20 Å20 Å2
2---57.0285 Å20 Å2
3----51.0876 Å2
Refinement stepCycle: LAST / Resolution: 4.036→14.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 3 0 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164448
X-RAY DIFFRACTIONf_angle_d1.026055
X-RAY DIFFRACTIONf_dihedral_angle_d16.1391519
X-RAY DIFFRACTIONf_chiral_restr0.056702
X-RAY DIFFRACTIONf_plane_restr0.005767
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1138X-RAY DIFFRACTIONPOSITIONAL
12B1138X-RAY DIFFRACTIONPOSITIONAL0.02
21A778X-RAY DIFFRACTIONPOSITIONAL
22B778X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.036-4.34060.2851850.3171657X-RAY DIFFRACTION61
4.3406-4.76470.28051360.26932749X-RAY DIFFRACTION100
4.7647-5.42530.25161480.24482771X-RAY DIFFRACTION100
5.4253-6.73090.31061360.26062806X-RAY DIFFRACTION100
6.7309-14.99470.21631580.21252861X-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)
1-0.6781-0.6924-1.27320.7479-0.50580.9955-0.4549-0.6628-1.1686-0.33760.8703-0.5735-0.32050.232201.61110.1732-0.16231.6914-0.01452.0766-44.8535-22.1311-54.2121
2-0.4396-0.1397-0.33521.3539-0.43020.44160.56260.2348-0.18140.4978-0.4185-0.34850.72280.251302.13370.0031-0.09192.09170.16131.5236-42.7943-13.8215-26.8073
30.009-0.1211-0.0189-0.0108-0.0426-0.098-0.18980.9204-1.02411.0192-0.1613-0.9252-0.3571-0.261402.5604-0.1782-0.00982.21930.04571.653-39.3414-9.1421-5.6577
40.04350.35980.15530.1227-0.01-0.24520.4115-0.8431.6027-1.65941.42230.0372.2482-0.398902.2029-0.33330.05052.840.27051.3569-45.6749-9.0727-15.3474
50.2721-0.1973-0.43860.4941-0.7066-0.09320.56120.2950.84880.8484-0.4239-0.0366-0.2134-0.395-02.03260.01140.14212.6685-0.17161.5603-39.5671-0.9398-15.7381
60.03570.2038-0.0201-0.0934-0.02380.2292-0.1284-1.76060.541-0.1274-0.90260.37550.2766-1.0373-01.38850.1441-0.1241.783-0.25221.2565-50.8325-6.8424-39.3887
72.25330.5972-0.18510.20350.96522.25650.08290.2151-0.1390.0548-0.08620.0162-0.0217-0.1490.13791.3915-0.05140.06541.443-0.0251.6617-63.8198-20.0001-70.7496
80.17620.20380.0661-0.13650.12860.04790.25520.8192-0.4369-1.55730.81570.7441.37440.325902.0837-0.11810.42572.0827-0.38052.2668-40.154-25.3241-80.5743
9-0.07350.0458-0.1386-0.1570.151-0.2552-0.64571.5645-0.2627-0.18072.00752.5634-0.7064-0.670102.271-0.18140.76822.6284-0.5543.096-87.2639-18.3312-62.6653
101.2291-0.531-2.2107-0.72992.101-0.0219-0.3702-0.3761-0.1514-0.64880.5273-0.4812-1.04510.075902.2359-0.2675-0.39141.45450.16071.2321-50.55953.5319-48.6307
11-0.2062-0.41870.31010.3224-0.80540.60280.0127-0.0395-0.3952-0.02540.0699-0.0184-1.1189-0.349101.92390.0872-0.29092.0842-0.28181.6522-38.953110.4868-26.8873
120.02390.0079-0.05750.10990.04730.0235-1.8296-1.949-0.04012.0445-1.2087-0.3401-0.69552.082302.7087-0.1049-0.39422.3101-0.05671.7761-43.78214.0443-5.787
130.1369-0.3945-0.24150.3937-0.0698-0.42381.60392.5445-0.67920.92561.34060.61530.75782.814802.62170.5191-0.34012.4139-0.47841.4136-43.80397.672-15.4546
14-0.1359-0.53260.16490.252-0.33130.1222-0.0454-0.44450.1934-0.3626-0.05421.0030.7092-0.393402.2830.1772-0.17971.40740.01691.4646-51.904313.811-15.9302
150.4171-0.34030.8383-0.1703-0.0030.2644-0.8646-0.5091-0.10231.2370.1961-0.51451.1953-0.228801.6429-0.46680.06550.9233-0.27961.1751-45.86222.4308-39.4851
162.4928-2.0238-0.47072.2569-0.12490.47510.2367-0.01070.2327-0.2637-0.0771-0.2714-0.01740.06540.05851.6083-0.0060.13381.5349-0.17761.904-33.6286-11.1592-70.7059
17-0.1208-0.02680.0763-0.0268-0.0669-0.00271.5747-0.6087-0.8391-1.1840.5381-1.2975-1.73651.4971-03.2684-1.08440.63112.7843-0.52053.5235-25.120512.0851-78.9934
18-0.10640.1627-0.0375-0.0210.28450.27440.9206-0.1258-2.3026-2.5553-0.89592.4364-0.90230.249901.76040.29850.28762.0264-0.02432.4175-39.9937-34.2515-63.9169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 12:43)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 44:71)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 72:81)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 82:100)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 101:120)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 121:137)
7X-RAY DIFFRACTION7(CHAIN A AND (RESID 138:182 OR RESID 194:274 OR RESID 286:299))
8X-RAY DIFFRACTION8(CHAIN A AND RESID 183:193)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 275:285)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 12:43)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 44:71)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 72:81)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 82:100)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 101:120)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 121:137)
16X-RAY DIFFRACTION16(CHAIN B AND (RESID 138:182 OR RESID 194:274 OR RESID 286:299))
17X-RAY DIFFRACTION17(CHAIN B AND RESID 183:193)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 275:285)

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