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- PDB-1eof: CRYSTAL STRUCTURE OF THE N136A MUTANT OF A SHAKER T1 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1eof
TitleCRYSTAL STRUCTURE OF THE N136A 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


monoatomic ion-gated channel activity / voltage-gated potassium channel activity / 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 / 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 ...Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / 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 / Resolution: 2.38 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)12,0541
Polymers12,0541
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.384, 59.384, 146.894
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: 12054.428 Da / Num. of mol.: 1 / Fragment: SHAKER T1 DOMAIN / Mutation: N136A
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 / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% Isopropanol, .1 M Hepes 7.5, .2 M MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.5 / 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: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→35 Å / Num. all: 5586 / Num. obs: 5586 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.9
Reflection shellResolution: 2.38→2.46 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.256 / % possible all: 100
Reflection
*PLUS
% possible obs: 98 % / Num. measured all: 81032

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.38→14.9 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1398820.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.264 241 4.8 %RANDOM
Rwork0.225 ---
all0.2319 5592 --
obs0.225 5049 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.02 Å2 / ksol: 0.3385 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å20 Å20 Å2
2--3.03 Å20 Å2
3----6.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.38→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 42 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 10 1.4 %
Rwork0.28 726 -
obs--81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.202 / % reflection Rfree: 1.4 % / Rfactor Rwork: 0.28

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