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- PDB-1k4c: Potassium Channel KcsA-Fab complex in high concentration of K+ -

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Basic information

Entry
Database: PDB / ID: 1k4c
TitlePotassium Channel KcsA-Fab complex in high concentration of K+
Components
  • (antibody Fab fragment ...) x 2
  • potassium channel KcsA
KeywordsMEMBRANE PROTEIN / K channel / protein-antibody Fab complex
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DIACYL GLYCEROL / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, Y. / Morais-Cabral, J.H. / Kaufman, A. / MacKinnon, R.
CitationJournal: Nature / Year: 2001
Title: Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution.
Authors: Zhou, Y. / Morais-Cabral, J.H. / Kaufman, A. / MacKinnon, R.
History
DepositionOct 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Remark 99Some fragments of disordered amino acids were built as solvent(water) molecules with the following ...Some fragments of disordered amino acids were built as solvent(water) molecules with the following sequence numbers: 106, 129, 165, 205, 206, 228, 251, 301, 309, 316, 318, 328, 330, 351, 365, 400, 408, 423 and 466. The water molecules 1, 2, 3, 4 are near the potassium ion pathway inside molecule KcsA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,10212
Polymers60,0593
Non-polymers1,0439
Water8,449469
1
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: potassium channel KcsA
hetero molecules

A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: potassium channel KcsA
hetero molecules

A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: potassium channel KcsA
hetero molecules

A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,40648
Polymers240,23412
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)155.330, 155.330, 76.270
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-3001-

K

21C-3002-

K

31C-3003-

K

41C-3004-

K

51C-3005-

K

61C-3006-

K

71C-3007-

K

81C-3014-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein potassium channel KcsA


Mass: 13211.582 Da / Num. of mol.: 1 / Fragment: potassium channel KcsA / Mutation: P2A, L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Production host: Escherichia coli (E. coli) / 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 , 4 types, 478 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 / Fragment: fragment of lipid / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


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


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: PEG 400, Magnesium Acetate, Sodium Acetate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 5.6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-15 mg/mlprotein1drop
220-25 %PEG4001reservoir
350 mMmagnesium acetate1reservoir
450 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 60798 / Num. obs: 60798 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rsym value: 0.071 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.53 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.53

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 3462539.1 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 5981 10 %RANDOM
Rwork0.218 ---
all-60790 --
obs-60790 99.1 %-
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 48 469 4534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.73
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2K_CNS.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMLIPID.TOP
X-RAY DIFFRACTION4LIPID2.PARK_XPLOR_TOP.TXT
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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