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- PDB-1s5h: Potassium Channel Kcsa-Fab Complex T75C mutant in K+ -

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Basic information

Entry
Database: PDB / ID: 1s5h
TitlePotassium Channel Kcsa-Fab Complex T75C mutant in K+
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / K+ CHANNEL / PROTEIN-ANTIBODY FAB COMPLEX / selectivity filter / ion occupancy
Function / homology
Function and homology information


voltage-gated potassium channel activity / voltage-gated potassium channel complex / monoatomic ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channel / 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 / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
Streptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMackinnon, R. / Zhou, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: A mutant KcsA K(+) channel with altered conduction properties and selectivity filter ion distribution.
Authors: Zhou, M. / MacKinnon, R.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,11412
Polymers60,0713
Non-polymers1,0439
Water4,107228
1
A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: Voltage-gated potassium channel
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: Voltage-gated potassium channel
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: Voltage-gated potassium channel
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,45448
Polymers240,28212
Non-polymers4,17236
Water21612
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)154.705, 154.705, 75.927
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-401-

K

21C-402-

K

31C-403-

K

41C-404-

K

51C-405-

K

61C-406-

K

71C-407-

K

81C-440-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Voltage-gated potassium channel /


Mass: 13223.636 Da / Num. of mol.: 1 / Mutation: P2A, T75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor, Streptomyces lividans
Genus: Streptomyces, Streptomyces / Species: , / Strain: , / Gene: KCSA, SKC1, SCO7660, SC10F4.33 / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: Q54397, UniProt: P0A333*PLUS

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Antibody , 2 types, 2 molecules AB

#1: 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)
#2: 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)

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Non-polymers , 4 types, 237 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


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


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: PEG 400, magnesium acetate, sodium acetate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2002
RadiationMonochromator: platinum-coated silicon mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→27.35 Å / Num. all: 45872 / Num. obs: 45718 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.054 / Net I/σ(I): 27
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4487 / Rsym value: 0.288 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4C

1k4c


Resolution: 2.2→27.35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2527612.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2259 5 %RANDOM
Rwork0.222 ---
all0.234 45524 --
obs0.222 45524 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7682 Å2 / ksol: 0.314808 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20 Å20 Å2
2--3.64 Å20 Å2
3----7.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 39 228 4207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_d0.82
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
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 383 5.1 %
Rwork0.262 7062 -
obs-7445 98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMLIPID_1.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4LIPID_1.PAR

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