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- PDB-6by3: Open and conductive conformation of KcsA-T75A mutant -

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Open data


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Basic information

Entry
Database: PDB / ID: 6by3
TitleOpen and conductive conformation of KcsA-T75A mutant
Components
  • Antibody Heavy ChainImmunoglobulin heavy chain
  • Antibody Light ChainImmunoglobulin light chain
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / KcsA / C-type inactivation / ion channel / potassium channel
Function / homology
Function and homology information


monoatomic ion transmembrane transport / plasma membrane
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
DIACYL GLYCEROL / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsLabro, A.J. / Cortes, D.M. / Tilegenova, C. / Cuello, L.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RO1GM097159-01A1 United States
Welch FoundationBI-1757 United States
American Heart AssociationAHA-11SDG5440003 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Inverted allosteric coupling between activation and inactivation gates in K+channels.
Authors: Labro, A.J. / Cortes, D.M. / Tilegenova, C. / Cuello, L.G.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,98511
Polymers56,9813
Non-polymers1,0048
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-22 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.126, 156.126, 74.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1002-

K

21C-1003-

K

31C-1004-

K

41C-1005-

K

51C-1006-

K

61C-1007-

K

71C-1116-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA


Mass: 10133.835 Da / Num. of mol.: 1 / Mutation: C28A, T75A, C90L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: kcsA, skc1, SCO7660, SC10F4.33 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A333

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody Heavy Chain / Immunoglobulin heavy chain


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Antibody Light Chain / Immunoglobulin light chain


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 132 molecules

#4: Chemical ChemComp-F09 / NONAN-1-OL / 1-Nonanol


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG400, 50 mM magnesium acetate, 50 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.92 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.92 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 38119 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.63 Å2 / Rmerge(I) obs: 0.153 / Χ2: 0.99 / Net I/σ(I): 13.8 / Num. measured all: 141801
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.35-2.393.60.44717150.877191.1
2.39-2.433.70.39719250.8761100
2.43-2.483.80.40819190.945199.8
2.48-2.533.70.31919010.923199.8
2.53-2.593.80.28719310.9411100
2.59-2.653.80.25719360.925199.9
2.65-2.713.70.24419121.002199.9
2.71-2.793.80.22319360.9761100
2.79-2.873.80.20919351.0581100
2.87-2.963.80.19218971.039199.9
2.96-3.073.80.18319311.078199.9
3.07-3.193.80.18219321.1411100
3.19-3.333.80.17919111.1471100
3.33-3.513.70.17419371.166199.8
3.51-3.733.70.16919191.126199.3
3.73-4.023.70.16619141.137198.9
4.02-4.423.70.16318571.065195.5
4.42-5.063.60.15818611.004195
5.06-6.373.60.14519350.814199
6.37-503.60.10419150.506195.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→36.799 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.03
RfactorNum. reflection% reflection
Rfree0.2188 1304 3.59 %
Rwork0.2052 --
obs0.2057 36352 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.81 Å2 / Biso mean: 58.3962 Å2 / Biso min: 25.48 Å2
Refinement stepCycle: final / Resolution: 2.37→36.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 47 124 4112
Biso mean--64.49 54.35 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034080
X-RAY DIFFRACTIONf_angle_d0.5725568
X-RAY DIFFRACTIONf_chiral_restr0.043639
X-RAY DIFFRACTIONf_plane_restr0.004702
X-RAY DIFFRACTIONf_dihedral_angle_d5.0212395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.46490.26971470.24893813396098
2.4649-2.5770.29951440.24963854399899
2.577-2.71290.2651450.23343857400299
2.7129-2.88280.25581390.237538744013100
2.8828-3.10530.28051420.23438954037100
3.1053-3.41750.2751480.22539214069100
3.4175-3.91160.21831450.202839224067100
3.9116-4.92630.18451490.174539264075100
4.9263-36.80370.17541450.19043986413199

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