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- PDB-1id1: CRYSTAL STRUCTURE OF THE RCK DOMAIN FROM E.COLI POTASSIUM CHANNEL -

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Basic information

Entry
Database: PDB / ID: 1id1
TitleCRYSTAL STRUCTURE OF THE RCK DOMAIN FROM E.COLI POTASSIUM CHANNEL
ComponentsPUTATIVE POTASSIUM CHANNEL PROTEIN
KeywordsMEMBRANE PROTEIN / RCK domain / E.coli Potassium Channel / BK Channel / Rossmann fold
Function / homology
Function and homology information


potassium channel activity / potassium ion transport / protein-containing complex / identical protein binding / plasma membrane
Similarity search - Function
: / TrkA-N domain / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / Potassium channel domain / Ion channel / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Voltage-gated potassium channel Kch
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJiang, Y. / Pico, A. / Cadene, M. / Chait, B.T. / MacKinnon, R.
CitationJournal: Neuron / Year: 2001
Title: Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel.
Authors: Jiang, Y. / Pico, A. / Cadene, M. / Chait, B.T. / MacKinnon, R.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE POTASSIUM CHANNEL PROTEIN
B: PUTATIVE POTASSIUM CHANNEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,4922
Polymers33,4922
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.51, 65.51, 110.24
Angle α, β, γ (deg.)90, 90, 90
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PUTATIVE POTASSIUM CHANNEL PROTEIN


Mass: 16746.068 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 241-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P31069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, sodium chloride, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mM1dropNaCl
410 %PEG40001reservoir
51-1.5 M1reservoirNaCl
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection shellResolution: 2.4→30 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.292

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 1818 random
Rwork0.208 --
all0.208 18219 -
obs0.208 17912 -
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 0 57 2320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.008

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