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- PDB-3eff: The Crystal Structure of Full-Length KcsA in its Closed Conformation -

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Basic information

Entry
Database: PDB / ID: 3eff
TitleThe Crystal Structure of Full-Length KcsA in its Closed Conformation
Components
  • (FAB) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / Full length KcsA / Bulge helix / Cell membrane / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich ...ATP synthase delta/epsilon subunit, C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsUysal, S. / Vasquez, V. / Tereshko, T. / Esaki, K. / Fellouse, F.A. / Sidhu, S.S. / Koide, S. / Perozo, E. / Kossiakoff, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of full-length KcsA in its closed conformation.
Authors: Uysal, S. / Vasquez, V. / Tereshko, V. / Esaki, K. / Fellouse, F.A. / Sidhu, S.S. / Koide, S. / Perozo, E. / Kossiakoff, A.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB
B: FAB
C: FAB
D: FAB
K: Voltage-gated potassium channel
L: Voltage-gated potassium channel
M: Voltage-gated potassium channel
N: Voltage-gated potassium channel


Theoretical massNumber of molelcules
Total (without water)156,6328
Polymers156,6328
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.799, 173.905, 339.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody FAB


Mass: 23493.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB


Mass: 23905.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein
Voltage-gated potassium channel


Mass: 15458.734 Da / Num. of mol.: 4 / Fragment: UNP residues 22-160 / Source method: isolated from a natural source / Source: (natural) Streptomyces lividans (bacteria) / References: UniProt: P0A334

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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: 5.45 Å3/Da / Density % sol: 77.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 340 mM (NH4)2SO4, 11% PEG4000, 100 mM Na3C6H5O7 pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→40 Å / Num. all: 34199 / Num. obs: 32412 / % possible obs: 94.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.108
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.85 / Num. unique all: 3849 / % possible all: 89.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→40 Å / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.331 1625 -RANDOM
Rwork0.27 ---
all0.29 34199 --
obs0.28 32412 94.8 %-
Refinement stepCycle: LAST / Resolution: 3.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10912 0 0 0 10912

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