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- PDB-1xl6: Intermediate gating structure 2 of the inwardly rectifying K+ cha... -

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Basic information

Entry
Database: PDB / ID: 1xl6
TitleIntermediate gating structure 2 of the inwardly rectifying K+ channel KirBac3.1
ComponentsInward rectifier potassium channel
KeywordsMETAL TRANSPORT / integral membrane protein / ion channel / inwardly rectifying K+ 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
: / SPERMINE / : / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGulbis, J.M. / Kuo, A. / Smith, B. / Doyle, D.A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M.
CitationJournal: To be Published
Title: Two intermediate gating state crystal structures of the KirBac3.1 K+ channel
Authors: Gulbis, J.M. / Kuo, A. / Smith, B. / Doyle, D.A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_ref_seq_dif.details / _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: Inward rectifier potassium channel
B: Inward rectifier potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,06611
Polymers67,5662
Non-polymers5009
Water1,04558
1
A: Inward rectifier potassium channel
B: Inward rectifier potassium channel
hetero molecules

A: Inward rectifier potassium channel
B: Inward rectifier potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,13222
Polymers135,1314
Non-polymers1,00118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area21040 Å2
ΔGint-128 kcal/mol
Surface area53040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.756, 107.532, 89.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1000-

K

21A-1001-

K

31A-1002-

K

41A-1003-

K

51A-1004-

K

61A-1006-

K

71A-2001-

MG

81B-1005-

K

91B-3001-

SPM

101B-3001-

SPM

111B-3001-

SPM

121A-2002-

HOH

131A-2003-

HOH

141B-3002-

HOH

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Components

#1: Protein Inward rectifier potassium channel / Inwardly rectifying K+ channel KirBac3.1 / COG1226: Kef-type K+ transport systems / predicted NAD- ...Inwardly rectifying K+ channel KirBac3.1 / COG1226: Kef-type K+ transport systems / predicted NAD-binding component


Mass: 33782.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)star / References: GenBank: 46201166, UniProt: D9N164*PLUS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE ARE THREE ALTERNATE ARRANGEMENTS OF IONS AND COORDINATED WATER MOLECULES. THEY ARE NOT ...THERE ARE THREE ALTERNATE ARRANGEMENTS OF IONS AND COORDINATED WATER MOLECULES. THEY ARE NOT COMPLETELY MUTUALLY EXCLUSIVE. THE FIRST INCLUDES K(1001), K(1003), K(1004) AND HOH(2002). THE SECOND INCLUDES K(1002), K(1003) AND K(1005). THE THIRD INCLUDES K(1002), K(1006), HOH(3002), MG(2001) AND HOH(2003). THERE ARE ALSO FOUR CONFORMERS OF THE SPERMINE MOLECULE (SPM L3001). ALTERNATE CONFORMERS HAVE BEEN FLAGGED E,F,G,H.

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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: 3.77 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 90mM Hepes, 2.5% PEG 8000, 2.5% PEG 4000, 20% PEG 400, 12.5mM magnesium chloride, 42.5mM magnesium acetate, 2.5% glycerol, 14mM Hega-10 , pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 28510

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
X-PLORrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7B

1p7b


Resolution: 2.85→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.31 1224 5 %
Rwork0.27 --
obs-25550 -
Refinement stepCycle: LAST / Resolution: 2.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 22 58 4692

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