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- PDB-1bl8: POTASSIUM CHANNEL (KCSA) FROM STREPTOMYCES LIVIDANS -

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Basic information

Entry
Database: PDB / ID: 1bl8
TitlePOTASSIUM CHANNEL (KCSA) FROM STREPTOMYCES LIVIDANS
ComponentsPROTEIN (POTASSIUM CHANNEL PROTEIN)
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNEL / INTEGRAL MEMBRANE PROTEIN
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.2 Å
AuthorsDoyle, D.A. / Cabral, J.M. / Pfuetzner, R.A. / Kuo, A. / Gulbis, J.M. / Cohen, S.L. / Chait, B.T. / Mackinnon, R.
CitationJournal: Science / Year: 1998
Title: The structure of the potassium channel: molecular basis of K+ conduction and selectivity.
Authors: Doyle, D.A. / Morais Cabral, J. / Pfuetzner, R.A. / Kuo, A. / Gulbis, J.M. / Cohen, S.L. / Chait, B.T. / MacKinnon, R.
History
DepositionJul 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 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_asym_id / _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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (POTASSIUM CHANNEL PROTEIN)
B: PROTEIN (POTASSIUM CHANNEL PROTEIN)
C: PROTEIN (POTASSIUM CHANNEL PROTEIN)
D: PROTEIN (POTASSIUM CHANNEL PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1297
Polymers41,0124
Non-polymers1173
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-75 kcal/mol
Surface area17310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.780, 68.930, 112.040
Angle α, β, γ (deg.)90.00, 124.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.1266, 0.92878, 0.34834), (-0.93119, -0.00973, 0.36439), (0.34183, -0.37051, 0.86364)31.41247, 86.76519, -12.10887
2given(-0.73691, -0.01034, 0.67591), (0.00458, -0.99994, -0.0103), (0.67598, -0.00449, 0.73691)112.17546, 53.01701, -43.35083
3given(0.13722, -0.93103, 0.33816), (0.92933, 0.00286, -0.36924), (0.3428, 0.36493, 0.86563)80.28391, -33.25713, -31.77395

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Components

#1: Protein
PROTEIN (POTASSIUM CHANNEL PROTEIN)


Mass: 10252.959 Da / Num. of mol.: 4 / Mutation: L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Plasmid: PQE60 / Gene (production host): KCSA / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 BLUE / References: UniProt: P0A334
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: 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: 6

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Sample preparation

CrystalDensity Matthews: 4.99 Å3/Da / Density % sol: 75.34 %
Crystal growpH: 7.5
Details: ONE-TO-MIXTURE OF PROTEIN SOLUTION AND RESERVOIR (200 MM CACL2, 100 MM HEPES PH 7.5, 48% PEG 400).
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
2150 mM1dropKCl
350 mMTris-HCl1drop
42 mMdithiothreitol1drop
5200 mM1reservoirCaCl2
6100 mMHEPES1reservoir
748 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 12603 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 2.3 % / % possible all: 66.6
Reflection shell
*PLUS
% possible obs: 66.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4PROGRAM SUITEmodel building
SHELXL-97model building
X-PLOR3.851refinement
CCP4phasing
SHELXL-97phasing
RefinementMethod to determine structure: MIR / Resolution: 3.2→10 Å / Isotropic thermal model: GROUP / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1252 10.4 %SHELL
Rwork0.28 ---
obs0.28 12054 93.3 %-
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 3 1 2824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.73
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.53
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.73
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.53

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