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- PDB-1eoe: CRYSTAL STRUCTURE OF THE V135R MUTANT OF A SHAKER T1 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1eoe
TitleCRYSTAL STRUCTURE OF THE V135R MUTANT OF A SHAKER T1 DOMAIN
ComponentsPOTASSIUM CHANNEL KV1.1
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNELS / APLYSIA KV1.1 / PROTON TRANSPORT
Function / homology
Function and homology information


delayed rectifier potassium channel activity / action potential / voltage-gated potassium channel complex / protein homooligomerization
Similarity search - Function
Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily ...Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.704 Å
AuthorsNanao, M.H. / Cushman, S.J. / Jahng, A.W. / DeRubeis, D. / Choe, S. / Pfaffinger, P.J.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Voltage dependent activation of potassium channels is coupled to T1 domain structure.
Authors: Cushman, S.J. / Nanao, M.H. / Jahng, A.W. / DeRubeis, D. / Choe, S. / Pfaffinger, P.J.
History
DepositionMar 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POTASSIUM CHANNEL KV1.1


Theoretical massNumber of molelcules
Total (without water)12,1561
Polymers12,1561
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.138, 60.138, 146.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein POTASSIUM CHANNEL KV1.1


Mass: 12155.516 Da / Num. of mol.: 1 / Fragment: SHAKER T1 DOMAIN / Mutation: V135R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: PET20 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q16968
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% Isopropanol, .1 M Hepes 7.5, .2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Bixby, K.A., (1999) Nature Struct. Biol., 6, 38.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %isopropanol1reservoir
20.2 M1reservoirMgCl2
30.1 MHEPES1reservoir
41 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 15106 / Num. obs: 15106 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 20.316 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / % possible all: 80.7
Reflection
*PLUS
Num. measured all: 130025

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing
RefinementResolution: 1.704→19.84 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: KONNERT-HENDRICKSON
RfactorNum. reflectionSelection details
Rfree0.2493 701 RANDOM
Rwork0.20804 --
all0.21854 13900 -
obs0.21854 13208 -
Refinement stepCycle: LAST / Resolution: 1.704→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 0 103 953
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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