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- PDB-2x6c: Potassium Channel from Magnetospirillum Magnetotacticum -

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Basic information

Entry
Database: PDB / ID: 2x6c
TitlePotassium Channel from Magnetospirillum Magnetotacticum
ComponentsATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
KeywordsMETAL TRANSPORT / INTEGRAL MEMBRANE PROTEIN / ION CHANNEL
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
: / PHOSPHOCHOLINE / SAMARIUM (III) ION / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsClarke, O.B. / Caputo, A.T. / Hill, A.P. / Vandenberg, J.I. / 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
DepositionFeb 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references / Refinement description ...Database references / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,93817
Polymers33,7261
Non-polymers1,21216
Water86548
1
A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)139,75168
Polymers134,9034
Non-polymers4,84864
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 area21040 Å2
ΔGint-239.3 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.518, 106.518, 88.854
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-1305-

K

21A-1306-

K

31A-1307-

K

41A-1308-

K

51A-1309-

K

61A-1310-

K

71A-1311-

K

81A-1312-

K

91A-1313-

K

101A-1314-

K

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33725.715 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-320
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HIS-TAG
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: D9N164*PLUS

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Non-polymers , 5 types, 64 molecules

#2: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sm
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625 C-TERMINAL HIS-TAG IN PRESENT ENTRY. ...RESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625 C-TERMINAL HIS-TAG IN PRESENT ENTRY. Q170 HAS BEEN MUTATED TO ALANINE.

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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: 4.25 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 7.5
Details: AS PER WWPDB ENTRY 2X6A, EXCEPT THE CRYSTAL WAS SOAKED WITH 2MM SMAC (FINAL CONCENTRATION IN THE DROP) FOR 16HRS PRIOR TO DATA COLLECTION., pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953694
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953694 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14682 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 64.86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WLH

2wlh


Resolution: 2.7→41.983 Å / SU ML: 0.49 / σ(F): 1.33 / Phase error: 23.06 / Stereochemistry target values: ML
Details: ANOMALOUS DIFFERENCE MAP WAS USED TO GUIDE THE PLACEMENT OF SAMARIUM IONS. THE INDIVIDUAL FRIEDELS (I+ AND I-) WERE USED AS INDEPENDENT REFLECTIONS DURING REFINEMENT BY PHENIX
RfactorNum. reflection% reflection
Rfree0.2609 1356 5 %
Rwork0.2187 --
obs0.2208 14682 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.245 Å2 / ksol: 0.274 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3208 Å20 Å20 Å2
2--1.3208 Å20 Å2
3----2.6417 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 26 48 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142138
X-RAY DIFFRACTIONf_angle_d1.252865
X-RAY DIFFRACTIONf_dihedral_angle_d22.2961241
X-RAY DIFFRACTIONf_chiral_restr0.082336
X-RAY DIFFRACTIONf_plane_restr0.004357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.696-2.79240.34321700.30192552X-RAY DIFFRACTION100
2.7924-2.90410.30521660.27362527X-RAY DIFFRACTION100
2.9041-3.03630.30591190.24632568X-RAY DIFFRACTION100
3.0363-3.19630.30421640.22392539X-RAY DIFFRACTION100
3.1963-3.39650.27191190.20642575X-RAY DIFFRACTION100
3.3965-3.65860.25891120.19542583X-RAY DIFFRACTION100
3.6586-4.02650.20951370.18772553X-RAY DIFFRACTION100
4.0265-4.60850.21721250.16662579X-RAY DIFFRACTION100
4.6085-5.80380.22571290.19122574X-RAY DIFFRACTION100
5.8038-41.98840.23841150.24042567X-RAY DIFFRACTION99
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)
10.7899-0.50640.08851.3934-0.42560.1358-0.1451-0.0632-0.09330.27860.9641-0.2341-1.55411.4205-0.52452.249-0.2661-0.05580.8734-0.12690.56322.0306-39.6311-36.4074
20.5525-0.48910.79220.9832-1.39251.946-0.131-0.3102-0.1560.55710.0986-0.1766-0.92412.55060.19640.5466-0.08250.02510.8678-0.15570.16056.7982-51.2912-54.0122
31.6746-0.2136-1.32212.1071-0.30682.55530.06030.02080.175-0.0632-0.10190.0518-0.03590.00440.00780.12710.0535-0.02590.161-0.00040.202320.179-62.5054-86.2816
40.7301-0.12080.05050.29471.1765.20480.11160.11760.8033-0.18260.35640.4648-2.680.3491-1.16561.5402-0.20110.75450.57540.25041.147827.611-39.9142-94.2948
53.9678-0.7379-0.53840.1535-0.00755.4849-0.7239-0.4091-2.5514-0.9546-0.1467-0.14452.5568-0.15720.91941.26590.09460.37720.550.18881.29116.3588-87.229-78.8206
66.34765.1023-0.76789.2058-2.94161.8597-0.25670.669-0.88130.4853-0.1341-1.4294-0.2296-0.20490.36990.2542-0.0822-0.02310.3436-0.0120.383727.4057-46.5158-76.8711
73.79310.8098-0.46981.015-2.55977.67181.2697-0.5449-0.02550.6042-0.9629-0.0443-3.0344.6234-0.02981.2643-1.339-0.11842.831-0.18550.473815.2062-45.4523-45.7818
81.99392.5202-5.71654.07060.08744.71271.6318-0.4186-0.091.370.41610.0108-4.00014.4195-1.38431.1845-0.5653-0.06611.4457-0.17350.22247.2008-47.4288-30.207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 111:119
2X-RAY DIFFRACTION2CHAIN A AND RESID 120:137
3X-RAY DIFFRACTION3CHAIN A AND (RESID 138:181 OR RESID 194:275 OR RESID 285:301)
4X-RAY DIFFRACTION4CHAIN A AND RESID 182:193
5X-RAY DIFFRACTION5CHAIN A AND RESID 276:284
6X-RAY DIFFRACTION6CHAIN A AND RESID 13:26
7X-RAY DIFFRACTION7CHAIN A AND RESID 30:70
8X-RAY DIFFRACTION8CHAIN A AND RESID 86:104

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