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- PDB-1t1d: CRYSTAL STRUCTURE OF THE TETRAMERIZATION DOMAIN OF THE SHAKER POT... -

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Basic information

Entry
Database: PDB / ID: 1t1d
TitleCRYSTAL STRUCTURE OF THE TETRAMERIZATION DOMAIN OF THE SHAKER POTASSIUM CHANNEL
ComponentsPROTEIN (POTASSIUM CHANNEL KV1.1)
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNELS / TETRAMERIZATION DOMAIN / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsKreusch, A. / Pfaffinger, P.J. / Stevens, C.F. / Choe, S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels.
Authors: Bixby, K.A. / Nanao, M.H. / Shen, N.V. / Kreusch, A. / Bellamy, H. / Pfaffinger, P.J. / Choe, S.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (POTASSIUM CHANNEL KV1.1)


Theoretical massNumber of molelcules
Total (without water)12,0971
Polymers12,0971
Non-polymers00
Water1,946108
1
A: PROTEIN (POTASSIUM CHANNEL KV1.1)

A: PROTEIN (POTASSIUM CHANNEL KV1.1)

A: PROTEIN (POTASSIUM CHANNEL KV1.1)

A: PROTEIN (POTASSIUM CHANNEL KV1.1)


Theoretical massNumber of molelcules
Total (without water)48,3904
Polymers48,3904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)59.710, 59.710, 146.860
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 PROTEIN (POTASSIUM CHANNEL KV1.1)


Mass: 12097.453 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Strain: BL21 (DE3) / Cell line: CENTRAL NERVOUS SYSTEM / 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 / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5
Details: 24% ISOPROPANOL, .2M MGCL2, .1 M HEPES PH 7.5, 1MM DTT
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.5 Msodium formate1reservoir
20.1 Mbis-Tris-propane1reservoir
30.2 M1reservoirMgCl2
40.15 M1reservoirNaCl
510 mMbeta-mercaptoethanol1reservoir
624 %isopropanol1drop
70.2 M1dropMgCl2
80.1 MHEPES1droppH7.5
91 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: PT-COATED-MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.51→25 Å / Num. obs: 26768 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 19.35 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.2
Reflection shellResolution: 1.51→1.54 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.16 / % possible all: 93.7
Reflection
*PLUS
Num. obs: 24631 / % possible obs: 93.7 % / Num. measured all: 135247 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
REFMACrefinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A68

1a68


Resolution: 1.51→19.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -5 %RANDOM
Rwork0.229 ---
obs-21355 92.1 %-
Refinement stepCycle: LAST / Resolution: 1.51→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 108 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3542
X-RAY DIFFRACTIONp_mcangle_it2.0493
X-RAY DIFFRACTIONp_scbond_it1.7612
X-RAY DIFFRACTIONp_scangle_it2.7553
X-RAY DIFFRACTIONp_plane_restr0.0192
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1380.3
X-RAY DIFFRACTIONp_planar_tor3.27
X-RAY DIFFRACTIONp_staggered_tor15.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2120
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_scangle_it3

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