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- PDB-7sqw: Structure of the KcsA-W67F mutant with the activation gate in the... -

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Basic information

Entry
Database: PDB / ID: 7sqw
TitleStructure of the KcsA-W67F mutant with the activation gate in the closed conformation
Components
  • (Antibody Fragment) x 2
  • KcsA potassium channel
KeywordsMEMBRANE PROTEIN / channel / Fab complex / C-type inactivation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-1EM / NONAN-1-OL / :
Function and homology information
Biological speciesMus musculus (house mouse)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.21 Å
AuthorsCuello, L.G. / Labro, A.J.
Funding support United States, Belgium, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097159 United States
Other governmentBOF Ghent University Belgium
CitationJournal: Sci Adv / Year: 2022
Title: The nonconducting W434F mutant adopts upon membrane depolarization an inactivated-like state that differs from wild-type Shaker-IR potassium channels.
Authors: Coonen, L. / Martinez-Morales, E. / Van De Sande, D.V. / Snyders, D.J. / Cortes, D.M. / Cuello, L.G. / Labro, A.J.
History
DepositionNov 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody Fragment
B: Antibody Fragment
C: KcsA potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,56910
Polymers57,7873
Non-polymers7827
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-32 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.962, 153.962, 75.804
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-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 KcsA potassium channel


Mass: 10939.700 Da / Num. of mol.: 1 / Mutation: W67F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Production host: Streptomyces (bacteria)

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody Fragment


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 Fragment


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 , 3 types, 7 molecules

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


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-1EM / (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE


Mass: 442.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: PEG400 , 50 mM magnesium acetate, 50 mM sodium acetate, 300 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.21→48.69 Å / Num. obs: 14014 / % possible obs: 99.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 81.33 Å2 / CC1/2: 0.75 / Net I/σ(I): 14.7
Reflection shellResolution: 3.21→48.69 Å / Num. unique obs: 14012 / CC1/2: 0.5 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 3.21→48.69 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 1401 10 %
Rwork0.2315 12613 -
obs0.2357 14014 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.2 Å2 / Biso mean: 89.551 Å2 / Biso min: 34.18 Å2
Refinement stepCycle: final / Resolution: 3.21→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 46 0 4056
Biso mean--72.59 --
Num. residues----534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.21-3.320.33381020.2927947104972
3.32-3.460.31340.2551201133592
3.46-3.610.3321430.25231262140596
3.62-3.810.34291380.24111284142299
3.81-4.040.28341480.251313141462100
4.04-4.350.281480.217313171465100
4.36-4.790.20961430.213913191462100
4.79-5.480.27071500.228913221472100
5.49-6.910.30271440.242413191463100
6.91-48.690.23981510.2131328147997
Refinement TLS params.Method: refined / Origin x: -27.6765 Å / Origin y: -19.5068 Å / Origin z: -27.4419 Å
111213212223313233
T0.3925 Å2-0.3197 Å2-0.0845 Å2-0.529 Å20.0002 Å2--0.4123 Å2
L0.312 °20.0278 °2-0.1548 °2-0.3131 °20.1143 °2--0.365 °2
S-0.0587 Å °0.0175 Å °-0.1051 Å °0.0144 Å °0.0434 Å °0.149 Å °0.5199 Å °-0.3258 Å °0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 219
2X-RAY DIFFRACTION1allB1 - 212
3X-RAY DIFFRACTION1allC22 - 124
4X-RAY DIFFRACTION1allC201 - 301
5X-RAY DIFFRACTION1allD1 - 5

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