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- PDB-1p7b: Crystal structure of an inward rectifier potassium channel -

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Basic information

Entry
Database: PDB / ID: 1p7b
TitleCrystal structure of an inward rectifier potassium channel
Componentsintegral membrane channel and cytosolic domains
KeywordsMETAL TRANSPORT / transmembrane helices / ion conduction / immunoglobulin fold / cytosolic assembly
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
: / Inward rectifier potassium channel
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.65 Å
AuthorsKuo, A. / Gulbis, J.M. / Antcliff, J.F. / Rahman, T. / Lowe, E.D. / Zimmer, J. / Cuthbertson, J. / Ashcroft, F.M. / Ezaki, T. / Doyle, D.A.
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
DepositionMay 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_asym_id / _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
Remark 999This protein has not been submitted to a major sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: integral membrane channel and cytosolic domains
B: integral membrane channel and cytosolic domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5116
Polymers74,3552
Non-polymers1564
Water1267
1
A: integral membrane channel and cytosolic domains
B: integral membrane channel and cytosolic domains
hetero molecules

A: integral membrane channel and cytosolic domains
B: integral membrane channel and cytosolic domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,02312
Polymers148,7104
Non-polymers3138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area17390 Å2
ΔGint-120 kcal/mol
Surface area47530 Å2
MethodPISA, PQS
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-402-

K

21A-403-

K

31A-404-

K

41B-401-

K

DetailsThe asymmetric unit contains a homodimer (chains A and B). The biological assembly is a homotetramer. To generate the tetramer from the asymmetric unit apply the operator (1-x,1-y,z) to A and B..

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Components

#1: Protein integral membrane channel and cytosolic domains


Mass: 37177.488 Da / Num. of mol.: 2
Fragment: potassium channel, c-terminal domain related to girk
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: chromosome 1 kirbac1.1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P83698
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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 %
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
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
250 mM1dropKCl
30.05 mMTris-DM1drop
49-12 mg/mlprotein1drop
520-22 %PEG4001reservoir
650-100 mMmagnesium acetate1reservoiror MgCl2
70.1 Mglycine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / 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. all: 14459 / Num. obs: 14455 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74.3 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 / Num. unique all: 2083 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 87944
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
MLPHAREphasing
DMmodel building
RAVEmodel building
CNSrefinement
CCP4(SCALA)data scaling
DMphasing
RAVEphasing
RefinementMethod to determine structure: MIR / Resolution: 3.65→7.5 Å / Cross valid method: Throughout the refinement. / σ(F): -3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Minimization with a maximum likelihood target applied iteratively between model-building cycles. Low temperature simulated annealing protocols with torsion angle refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.329 638 -5 % of reflections were selected in thin resolution shells
Rwork0.295 ---
all0.297 12777 --
obs0.297 12773 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--33.184 Å20 Å20 Å2
2---16.813 Å20 Å2
3---49.996 Å2
Refinement stepCycle: LAST / Resolution: 3.65→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 4 7 4059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.5
LS refinement shellResolution: 3.65→3.85 Å / Rfactor Rfree error: 0.037
RfactorNum. reflection% reflection
Rfree0.399 116 -
Rwork0.348 --
obs-1980 100 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.5 Å / σ(F): -3 / % reflection Rfree: 5 % / Rfactor obs: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2
LS refinement shell
*PLUS
Rfactor Rfree: 0.399 / Rfactor Rwork: 0.348

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