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- PDB-2aem: Crystal Structures of the MthK RCK Domain -

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Basic information

Entry
Database: PDB / ID: 2aem
TitleCrystal Structures of the MthK RCK Domain
ComponentsCalcium-gated potassium channel mthK
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN / Rossmann fold / helix-turn-helix
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. ...Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDong, J. / Shi, N. / Berke, I. / Chen, L. / Jiang, Y.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structures of the MthK RCK Domain and the Effect of Ca2+ on Gating Ring Stability
Authors: Dong, J. / Shi, N. / Berke, I. / Chen, L. / Jiang, Y.
#1: Journal: Nature / Year: 2002
Title: Crystal structure and mechanism of a calcium-gated potassium channel
Authors: Jiang, Y. / Lee, A. / Chen, J. / Cadene, M. / Chait, B.T. / MacKinnon, R.
History
DepositionJul 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / 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: Calcium-gated potassium channel mthK


Theoretical massNumber of molelcules
Total (without water)25,9151
Polymers25,9151
Non-polymers00
Water905
1
A: Calcium-gated potassium channel mthK

A: Calcium-gated potassium channel mthK


Theoretical massNumber of molelcules
Total (without water)51,8292
Polymers51,8292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_546y+1/3,x-1/3,-z+5/31
Buried area7180 Å2
ΔGint-42 kcal/mol
Surface area19130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)164.880, 164.880, 82.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-4-

HOH

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Components

#1: Protein Calcium-gated potassium channel mthK


Mass: 25914.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: O27564
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.17 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 400, Ammonium sulfate, cacodylate , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→35.8 Å / Num. all: 10766 / Num. obs: 10728 / % possible obs: 99.7 % / Observed criterion σ(I): 2.77 / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 23
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.524 / Num. unique all: 1068 / Rsym value: 0.524 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LNQ

1lnq


Resolution: 2.8→35.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 542 -RANDOM
Rwork0.2242 ---
all0.226 10749 --
obs0.226 10711 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 0 5 1742

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