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- PDB-3gb7: Potassium Channel KcsA-Fab complex in Li+ -

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Basic information

Entry
Database: PDB / ID: 3gb7
TitlePotassium Channel KcsA-Fab complex in Li+
Components
  • (antibody Fab fragment ...) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / ion-channel / ion selectivity / potassium transport / lithium block / integral membrane protein / voltage-gated potassium channel / Cell membrane / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


voltage-gated potassium channel activity / identical protein binding / 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 / NICKEL (II) ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsThompson, A.N. / Ilsoo, K. / Panosian, T.D. / Iverson, T.M. / Allen, T.W. / Nimigean, C.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore.
Authors: Thompson, A.N. / Kim, I. / Panosian, T.D. / Iverson, T.M. / Allen, T.W. / Nimigean, C.M.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)60,7425
Polymers60,0593
Non-polymers6842
Water905
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)242,96920
Polymers240,23412
Non-polymers2,7358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area3500 Å2
ΔGint-24 kcal/mol
Surface area19900 Å2
Unit cell
Length a, b, c (Å)157.064, 157.064, 75.616
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-125-

NI

21C-126-

HOH

31C-127-

HOH

41C-128-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Voltage-gated potassium channel


Mass: 13211.582 Da / Num. of mol.: 1 / Mutation: P2A, L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pASK90 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / 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, 7 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24% PEG 400, 100 mM MES, 50 mM Magnesium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 21675 / Num. obs: 20652 / % possible obs: 95.5 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 3 % / Biso Wilson estimate: 100.7 Å2 / Rsym value: 0.04 / Net I/σ(I): 25.2

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4D

1k4d


Resolution: 2.85→19.66 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1825785.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1047 5.1 %RANDOM
Rwork0.239 ---
obs0.239 20652 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1902 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 79 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2--2.79 Å20 Å2
3----5.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.85→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 32 5 4111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.85→2.95 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.391 101 4.8 %
Rwork0.368 2014 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dga.pardga.top

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