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- PDB-1xl4: Intermediate gating structure 1 of the inwardly rectifying K+ cha... -

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Basic information

Entry
Database: PDB / ID: 1xl4
TitleIntermediate gating structure 1 of the inwardly rectifying K+ channel KirBac3.1
ComponentsInward rectifier potassium channelInward-rectifier potassium channel
KeywordsMETAL TRANSPORT / integral membrane protein / ion channel / inwardly rectifying K+ channel
Function / homology
Function and homology information


inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / membrane => GO:0016020 / 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
: / : / ATP-sensitive inward rectifier potassium channel 10
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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

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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)67,7858
Polymers67,5662
Non-polymers2206
Water3,243180
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)135,57116
Polymers135,1314
Non-polymers44012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area21070 Å2
ΔGint-128 kcal/mol
Surface area50790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.627, 109.385, 88.786
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-2001-

MG

71A-2002-

HOH

81A-2003-

HOH

91B-2002-

HOH

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Components

#1: Protein Inward rectifier potassium channel / 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: Q2W6R1*PLUS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE ARE TWO ALTERNATE ARRANGEMENTS OF IONS AND COORDINATED WATER MOLECULES. THE FIRST INCLUDES ...THERE ARE TWO ALTERNATE ARRANGEMENTS OF IONS AND COORDINATED WATER MOLECULES. THE FIRST INCLUDES K(A1001), K(A1003), HOH(A2002), MG(A2001) AND HOH(B2002). THE SECOND INCLUDES K(A1002), K(A1004) AND HOH(A2003).

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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: 3.8 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: 2.6→26 Å / Num. obs: 29551

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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: 2.6→12 Å / Cross valid method: Brunger / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1525 5 %Random
Rwork0.226 ---
all-29249 --
obs-27724 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.752 Å20 Å20 Å2
2---3.714 Å20 Å2
3---7.466 Å2
Refinement stepCycle: LAST / Resolution: 2.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 6 180 4673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.26
X-RAY DIFFRACTIONx_mcbond_it1.6951.5
X-RAY DIFFRACTIONx_mcangle_it2.0862
X-RAY DIFFRACTIONx_scbond_it2.9722
X-RAY DIFFRACTIONx_scangle_it3.2432.5

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