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- PDB-1a68: CRYSTAL STRUCTURE OF THE TETRAMERIZATION DOMAIN OF THE SHAKER POT... -

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Basic information

Entry
Database: PDB / ID: 1a68
TitleCRYSTAL STRUCTURE OF THE TETRAMERIZATION DOMAIN OF THE SHAKER POTASSIUM CHANNEL
ComponentsPOTASSIUM CHANNEL KV1.1
KeywordsPOTASSIUM CHANNELS / TETRAMERIZATION DOMAIN / APLYSIA KV1.1
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKreusch, A. / Pfaffinger, P.J. / Stevens, C.F. / Choe, S.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of the tetramerization domain of the Shaker potassium channel.
Authors: Kreusch, A. / Pfaffinger, P.J. / Stevens, C.F. / Choe, S.
History
DepositionMar 6, 1998Processing site: BNL
Revision 1.0Jun 10, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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)11,4941
Polymers11,4941
Non-polymers00
Water63135
1
A: POTASSIUM CHANNEL KV1.1

A: POTASSIUM CHANNEL KV1.1

A: POTASSIUM CHANNEL KV1.1

A: POTASSIUM CHANNEL KV1.1


Theoretical massNumber of molelcules
Total (without water)45,9764
Polymers45,9764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)51.034, 51.034, 65.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein POTASSIUM CHANNEL KV1.1


Mass: 11493.914 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION DOMAIN / Mutation: INSERTED MET AT N-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Tissue: CENTRAL NERVOUS SYSTEM / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: PET20B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / 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.: 35 / 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 Å3/Da / Density % sol: 39 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 7-8% PEG8000, 300 MM NACL, 200MM MGCL2, 20 MM TRIS, PH 8.5
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-8 %PEG800011
2300 mM11NaCl
3200 mM11MgCl2
420 mMTris-HCl11

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9799
DetectorType: SIEMENS / Detector: CCD AREA DETECTOR / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 7712 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 10.9 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.035 / % possible all: 97.2
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.035

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 612 7.9 %RANDOM
Rwork0.2 ---
obs0.2 7712 99 %-
Displacement parametersBiso mean: 26.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms742 0 0 35 777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.14
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.071.5
X-RAY DIFFRACTIONx_mcangle_it3.422
X-RAY DIFFRACTIONx_scbond_it3.52
X-RAY DIFFRACTIONx_scangle_it5.32.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 97 7.8 %
Rwork0.334 1145 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.14
LS refinement shell
*PLUS
Rfactor obs: 0.334

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