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- PDB-2pnv: Crystal Structure of the leucine zipper domain of small-conductan... -

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Basic information

Entry
Database: PDB / ID: 2pnv
TitleCrystal Structure of the leucine zipper domain of small-conductance Ca2+-activated K+ (SKCa) channel from Rattus norvegicus
ComponentsSmall conductance calcium-activated potassium channel protein 2
KeywordsMEMBRANE PROTEIN / leucine zipper / SKCa channel / Rattus norvegicus
Function / homology
Function and homology information


Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / positive regulation of potassium ion transport / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / regulation of neuronal synaptic plasticity / alpha-actinin binding / smooth endoplasmic reticulum ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / positive regulation of potassium ion transport / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / regulation of neuronal synaptic plasticity / alpha-actinin binding / smooth endoplasmic reticulum / potassium ion transmembrane transport / T-tubule / modulation of chemical synaptic transmission / potassium ion transport / sarcolemma / Z disc / postsynaptic membrane / dendritic spine / calmodulin binding / protein domain specific binding / neuronal cell body / glutamatergic synapse / cell surface / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKim, J.Y. / Kim, M.K. / Kang, G.B. / Park, C.S. / Eom, S.H.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the leucine zipper domain of small-conductance Ca2+-activated K+ (SK(Ca)) channel from Rattus norvegicus.
Authors: Kim, J.Y. / Kim, M.K. / Kang, G.B. / Park, C.S. / Eom, S.H.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small conductance calcium-activated potassium channel protein 2
B: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)9,9092
Polymers9,9092
Non-polymers00
Water724
1
A: Small conductance calcium-activated potassium channel protein 2

A: Small conductance calcium-activated potassium channel protein 2

A: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)14,8643
Polymers14,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area3900 Å2
ΔGint-40 kcal/mol
Surface area7480 Å2
MethodPISA
2
B: Small conductance calcium-activated potassium channel protein 2

B: Small conductance calcium-activated potassium channel protein 2

B: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)14,8643
Polymers14,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area3900 Å2
ΔGint-33 kcal/mol
Surface area7630 Å2
MethodPISA
3
A: Small conductance calcium-activated potassium channel protein 2

A: Small conductance calcium-activated potassium channel protein 2

A: Small conductance calcium-activated potassium channel protein 2

B: Small conductance calcium-activated potassium channel protein 2

B: Small conductance calcium-activated potassium channel protein 2

B: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)29,7286
Polymers29,7286
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation4_444-x-1,-y-1,z-1/21
crystal symmetry operation5_544y,-x+y-1,z-1/21
crystal symmetry operation6_554x-y,x,z-1/21
Buried area8900 Å2
ΔGint-83 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.200, 29.200, 192.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein/peptide Small conductance calcium-activated potassium channel protein 2 / SK2 / small-conductance Ca2+-activated K+ (SKCa) channel


Mass: 4954.655 Da / Num. of mol.: 2 / Fragment: leucine zipper domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnn2 / Plasmid: modified pGEX vector / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P70604
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.257 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate (pH 5.6), 20-22% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Nov 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.35
ReflectionResolution: 2.1→50 Å / Num. all: 5216 / Num. obs: 5204 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 68.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 8.2 / Num. unique all: 232 / Rsym value: 0.324 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C94

1c94


Resolution: 2.1→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.35. THE R-FACTOR IS 0.210 AND THE R-FREE IS 0.278 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 231 -RANDOM
Rwork0.21 ---
all0.215 5216 --
obs0.215 5204 99.8 %-
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--9.748 Å2-5.371 Å20 Å2
2---9.748 Å20 Å2
3---19.496 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms634 0 0 4 638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d14.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.046
RfactorNum. reflection% reflection
Rfree0.331 52 -
Rwork0.355 --
obs-766 95.3 %

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