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- PDB-2itc: Potassium Channel KcsA-Fab complex in Sodium Chloride -

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Basic information

Entry
Database: PDB / ID: 2itc
TitlePotassium Channel KcsA-Fab complex in Sodium Chloride
Components
  • Antibody Fab fragment heavy chain
  • Antibody Fab fragment light chain
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / Voltage-gated channel / Transmembrane / Ionic channel / Ion transport / K Channel / protein-antibody Fab complex
Function / homology
Function and homology information


monoatomic ion transmembrane transport / 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
pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLockless, S.W. / Zhou, M. / MacKinnon, R.
CitationJournal: Plos Biol. / Year: 2007
Title: Structural and Thermodynamic Properties of Selective Ion Binding in a K(+) Channel.
Authors: Lockless, S.W. / Zhou, M. / Mackinnon, R.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 999SEQUENCE Sequencing of the DNA construct shows that position 2 of chain C is an ALA.

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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)60,1055
Polymers60,0593
Non-polymers462
Water181
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)240,41820
Polymers240,23412
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Unit cell
Length a, b, c (Å)155.501, 155.501, 75.820
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-

NA

21C-126-

NA

31C-127-

HOH

DetailsThe biological assembly is generated from the following operators: x,y,z -x+2,-y,z y+1,-x+1,z -y+1,x-1,z

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Components

#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)
#3: Protein Voltage-gated potassium channel /


Mass: 13211.582 Da / Num. of mol.: 1 / Fragment: residues 1-124 / Mutation: L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue(DE3) / References: UniProt: P0A334
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / 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: 3.81 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% PEG400, 50 mM MgAcetate, 150 mM NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15167 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.088 / Χ2: 1.071 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.2-3.313.90.46914970.771100
3.31-3.453.90.34715260.832100
3.45-3.63.90.24714940.862100
3.6-3.793.90.18515230.95100
3.79-4.033.90.13515040.91100
4.03-4.343.90.09115131.005100
4.34-4.783.80.07315251.357100
4.78-5.473.80.06915201.32699.9
5.47-6.893.70.06215401.332100
6.89-503.80.03615251.497.1

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Phasing

Phasing MRRfactor: 0.419 / Cor.coef. Fo:Fc: 0.638
Highest resolutionLowest resolution
Rotation3 Å42.79 Å
Translation3 Å42.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→42.79 Å / Rfactor Rfree error: 0.01 / FOM work R set: 0.809 / Data cutoff high absF: 2263832 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 748 5 %RANDOM
Rwork0.246 ---
obs-15072 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.223 Å2 / ksol: 0.24 e/Å3
Displacement parametersBiso mean: 85.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.76 Å20 Å20 Å2
2--7.76 Å20 Å2
3----15.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 2 1 4077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.444 50 4 %
Rwork0.343 1212 -
obs-1262 45.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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