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- PDB-8thn: KcsA M96V mutant with Y78ester in High K+ -

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Basic information

Entry
Database: PDB / ID: 8thn
TitleKcsA M96V mutant with Y78ester in High K+
Components
  • KcsA Fab Heavy Chain
  • KcsA Fab Light Chain
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / Ion transport / Potassium ion channel / ester
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
: / TETRABUTYLAMMONIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsReddi, R. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Y1-GM-1104 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds.
Authors: Reddi, R. / Chatterjee, S. / Matulef, K. / Gustafson, A. / Gao, L. / Valiyaveetil, F.I.
History
DepositionJul 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,2048
Polymers57,8053
Non-polymers3995
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.587, 155.587, 75.718
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-201-

K

21C-202-

K

31C-203-

K

41C-204-

K

51C-205-

TBA

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Components

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Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10957.671 Da / Num. of mol.: 1 / Mutation: M96V, Y78ester
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody KcsA Fab 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: Homo sapiens (human)
#2: Antibody KcsA Fab 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: Homo sapiens (human)

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Non-polymers , 3 types, 6 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION


Mass: 242.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H36N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 27% PEG 400 (v/v), 50 mM magnesium acetate, 50 mM MES pH 6.25
PH range: 6.0- 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→55.01 Å / Num. obs: 20234 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.98 / Net I/σ(I): 5.1
Reflection shellResolution: 2.9→3.08 Å / Num. unique obs: 3264 / CC1/2: 0.365

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→55.01 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 2012 9.97 %
Rwork0.246 --
obs0.249 20171 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→55.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 21 1 4040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024134
X-RAY DIFFRACTIONf_angle_d0.4935650
X-RAY DIFFRACTIONf_dihedral_angle_d11.6461435
X-RAY DIFFRACTIONf_chiral_restr0.04649
X-RAY DIFFRACTIONf_plane_restr0.004714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.42911330.40791276X-RAY DIFFRACTION98
2.97-3.050.38551400.37921294X-RAY DIFFRACTION99
3.05-3.140.35761380.36231292X-RAY DIFFRACTION100
3.14-3.240.35531300.32521282X-RAY DIFFRACTION100
3.24-3.360.33511490.31631287X-RAY DIFFRACTION100
3.36-3.490.34791420.29521281X-RAY DIFFRACTION100
3.5-3.650.28051500.2541308X-RAY DIFFRACTION100
3.65-3.850.24591550.24681275X-RAY DIFFRACTION100
3.85-4.090.27221260.2251314X-RAY DIFFRACTION100
4.09-4.40.24981630.20161278X-RAY DIFFRACTION100
4.4-4.850.23341410.18751311X-RAY DIFFRACTION100
4.85-5.550.24891390.19091322X-RAY DIFFRACTION100
5.55-6.980.22121640.20281287X-RAY DIFFRACTION100
6.99-55.010.23661420.21311352X-RAY DIFFRACTION99

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