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- PDB-1jvm: KCSA POTASSIUM CHANNEL WITH TBA (TETRABUTYLAMMONIUM) AND RUBIDIUM -

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Basic information

Entry
Database: PDB / ID: 1jvm
TitleKCSA POTASSIUM CHANNEL WITH TBA (TETRABUTYLAMMONIUM) AND RUBIDIUM
ComponentsVoltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNEL / METAL TRANSPORT
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 / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RUBIDIUM ION / TETRABUTYLAMMONIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMorais-Cabral, J.H. / Zhou, Y. / MacKinnon, R.
CitationJournal: Nature / Year: 2001
Title: Energetic optimization of ion conduction rate by the K+ selectivity filter.
Authors: Morais-Cabral, J.H. / Zhou, Y. / MacKinnon, R.
History
DepositionAug 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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

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Assembly

Deposited unit
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9348
Polymers53,4354
Non-polymers4994
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-106 kcal/mol
Surface area17040 Å2
MethodPISA
2
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules

A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,86816
Polymers106,8708
Non-polymers9988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area16920 Å2
ΔGint-164 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.800, 69.400, 112.700
Angle α, β, γ (deg.)90.00, 125.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Voltage-gated potassium channel


Mass: 13358.756 Da / Num. of mol.: 4 / Fragment: Residues 1-125 / Mutation: P2A,L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P0A334
#2: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION


Mass: 242.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36N
#4: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG400,calcium chloride, Hepes, potassium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES1reservoirpH7.5
2120-300 mM1reservoirCaCl2
335-50 %PEG4001reservoir
45 mMLDAO1drop
550 mMTris1droppH7.5
62 mMdithiothreitol1drop
75 mMTBA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 22300 / Num. obs: 14799 / % possible obs: 0.664 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 21
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.088 / % possible all: 0.167
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Rmerge(I) obs: 0.088

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1BL8

1bl8


Resolution: 2.8→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3021 1485 10 %thin shells
Rwork0.281 ---
all0.29 20254 --
obs0.29 14477 --
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 12 1 2835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39362
X-RAY DIFFRACTIONc_bond_d0.0099
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.29 / Rfactor obs: 0.281 / Rfactor Rfree: 0.3021 / Rfactor Rwork: 0.281
Solvent computation
*PLUS
Displacement parameters
*PLUS

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