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- PDB-3stz: KcsA potassium channel mutant Y82C with nitroxide spin label -

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Basic information

Entry
Database: PDB / ID: 3stz
TitleKcsA potassium channel mutant Y82C with nitroxide spin label
Components
  • (antibody Fab fragment ...) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / Transmembrane protein / Ion channel / KcsA potassium channel / Inactivation / Spin-label
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chem-MTN / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRaghuraman, H. / Cordero-Morales, J. / Jogini, V. / Perozo, E.
CitationJournal: Structure / Year: 2012
Title: Mechanism of Cd(2+) Coordination during Slow Inactivation in Potassium Channels.
Authors: Raghuraman, H. / Cordero-Morales, J.F. / Jogini, V. / Pan, A.C. / Kollewe, A. / Roux, B. / Perozo, E.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1489
Polymers57,6893
Non-polymers4606
Water724
1
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: Voltage-gated potassium channel
hetero molecules

A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: Voltage-gated potassium channel
hetero molecules

A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: Voltage-gated potassium channel
hetero molecules

A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,59436
Polymers230,75412
Non-polymers1,83924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Unit cell
Length a, b, c (Å)155.732, 155.732, 76.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-202-

K

21C-203-

K

31C-204-

K

41C-205-

K

51C-206-

K

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Voltage-gated potassium channel /


Mass: 10841.644 Da / Num. of mol.: 1 / Mutation: Y82C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 Gold / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody antibody Fab fragment heavy chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody Fab fragment light chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: 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: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20-25% PEG400, 50mM magnesium acetate, 50mM sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 31708 / Num. obs: 29442 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / σ(F): 2
RfactorNum. reflection
Rfree0.285 2882
Rwork0.246 -
all-31708
obs-29442
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 17 4 4074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbonds0.007
X-RAY DIFFRACTIONangles1.41

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