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- PDB-2x6b: Potassium Channel from Magnetospirillum Magnetotacticum -

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Basic information

Entry
Database: PDB / ID: 2x6b
TitlePotassium Channel from Magnetospirillum Magnetotacticum
ComponentsATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
KeywordsMETAL TRANSPORT / ION CHANNEL / INTEGRAL MEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / 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 / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 / Non-polymer description ...Database references / Non-polymer description / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,1646
Polymers33,7261
Non-polymers4395
Water181
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)136,65824
Polymers134,9034
Non-polymers1,75520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area19150 Å2
ΔGint-117.6 kcal/mol
Surface area52200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.798, 104.798, 88.417
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-1301-

BA

21A-1302-

K

31A-1303-

K

41A-1305-

K

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Components

#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
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#5: 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 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: THE CRYSTAL WAS OBTAINED UNDER THE SAME CONDITIONS AS PDB ENTRY 2X6A, BUT SOAKED WITH BARIUM CHLORIDE (5MM FINAL CONCENTRATION) FOR 16HRS PRIOR TO CRYOCOOLING AND DATA COLLECTION, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.54975
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54975 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 14195 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 96.54 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % 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: 3.3→41.409 Å / SU ML: 0.43 / σ(F): 1.91 / Phase error: 31.16 / Stereochemistry target values: ML
Details: PHOSPHOCHOLINE IN STUCTURE REPRESENTS ZWITTERIONIC HEAD-GROUP OF FOS-CHOLINE DETERGENT FROM CRYSTALLISATION CONDITION.
RfactorNum. reflection% reflection
Rfree0.2919 643 4.5 %
Rwork0.2343 --
obs0.2368 14168 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.559 Å2 / ksol: 0.258 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3216 Å20 Å20 Å2
2--3.3216 Å20 Å2
3----6.6431 Å2
Refinement stepCycle: LAST / Resolution: 3.3→41.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 15 1 2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0282323
X-RAY DIFFRACTIONf_angle_d1.0193134
X-RAY DIFFRACTIONf_dihedral_angle_d22.0551357
X-RAY DIFFRACTIONf_chiral_restr0.066361
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2981-3.55270.40441130.28342693X-RAY DIFFRACTION99
3.5527-3.90990.34141330.24162732X-RAY DIFFRACTION100
3.9099-4.47510.30391350.20282677X-RAY DIFFRACTION100
4.4751-5.63590.2251410.17732697X-RAY DIFFRACTION100
5.6359-41.41260.29171210.27212726X-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)
12.0937-0.36690.52832.99871.92251.492-0.0646-0.7763-0.09211.17950.26910.12131.4815-0.7069-0.20041.3108-0.11910.07260.77210.22610.4307-7.5941.427648.4564
25.3271-2.23191.83962.5156-0.02665.22640.1708-0.4476-0.6833-0.0045-0.16971.0363-0.5964-0.4847-0.00070.8465-0.0380.12260.8382-0.05131.0543-29.088444.323710.3888
33.04410.56331.76321.27890.68163.4744-0.1081-0.245-0.1981-0.18910.1168-0.55490.12-0.18780.00390.54550.05050.03170.44760.09160.6167-21.096960.26582.5826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 34:137
2X-RAY DIFFRACTION2CHAIN A AND RESID 8:27
3X-RAY DIFFRACTION3CHAIN A AND RESID 138:301

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