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- PDB-2itd: Potassium Channel KcsA-Fab complex in Barium Chloride -

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Basic information

Entry
Database: PDB / ID: 2itd
TitlePotassium Channel KcsA-Fab complex in Barium Chloride
Components
  • Voltage-gated potassium channel
  • antibody Fab fragment heavy chain
  • antibody Fab fragment light chain
KeywordsMEMBRANE PROTEIN / Voltage-gated channel / Transmembrane / Ionic channel / Ion transport / 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
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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.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 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

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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)60,3335
Polymers60,0593
Non-polymers2752
Water57632
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)241,33320
Polymers240,23412
Non-polymers1,0998
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)156.075, 156.075, 75.424
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-

BA

21C-126-

BA

31C-127-

HOH

DetailsThe biological assembly is generated from the following operators: x,y,z -x+1,-y+1,z -y+1,x,y y,-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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P0A334
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 21% PEG400, 50 mM MgAcetate, 5 mM BaCl2, 150 mM NaCl, pH 6.2, 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: Sep 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 28012 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.535 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.88.40.4924860.914100
2.8-2.918.30.34824660.963100
2.91-3.048.40.2425110.995100
3.04-3.28.30.16124751.08100
3.2-3.48.40.11724991.164100
3.4-3.668.30.08624931.34100
3.66-4.038.30.07125071.703100
4.03-4.628.20.06525172.498100
4.62-5.828.10.06125302.621100
5.82-1007.90.04425152.13297.6

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Phasing

Phasing MRRfactor: 0.379 / Cor.coef. Fo:Fc: 0.728
Highest resolutionLowest resolution
Rotation3 Å42.82 Å
Translation3 Å42.82 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: 2.7→42.83 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1206 -Random
Rwork0.241 ---
obs-28012 99.8 %-
Displacement parametersBiso mean: 62.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 2 32 4108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.369 190 -
Rwork0.348 --
obs-3938 100 %

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