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- PDB-1otu: Structure of the Escherichia coli ClC Chloride channel E148Q muta... -

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Basic information

Entry
Database: PDB / ID: 1otu
TitleStructure of the Escherichia coli ClC Chloride channel E148Q mutant and Fab Complex
Components
  • Fab fragment (Heavy chain)
  • Fab fragment (Light chain)
  • Voltage-gated ClC-type chloride channel eriC
KeywordsMEMBRANE PROTEIN / ion channel / ClC chloride channel / Fab complex
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex / immunoglobulin mediated immune response / chloride transmembrane transport / proton transmembrane transport / B cell differentiation / antigen binding / blood microparticle ...chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex / immunoglobulin mediated immune response / chloride transmembrane transport / proton transmembrane transport / B cell differentiation / antigen binding / blood microparticle / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ig heavy chain V region T601 / Immunoglobulin kappa constant / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDutzler, R. / Campbell, E.B. / MacKinnon, R.
CitationJournal: Science / Year: 2003
Title: Gating the Selectivity Filter in ClC Chloride Channels
Authors: Dutzler, R. / Campbell, E.B. / MacKinnon, R.
History
DepositionMar 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated ClC-type chloride channel eriC
B: Voltage-gated ClC-type chloride channel eriC
C: Fab fragment (Heavy chain)
D: Fab fragment (Light chain)
E: Fab fragment (Heavy chain)
F: Fab fragment (Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,35112
Polymers193,1386
Non-polymers2136
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.113, 96.090, 170.284
Angle α, β, γ (deg.)90.00, 131.39, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly for the ClC channel is a dimer formed by chain A and B / C and D are the heavy and light chain of a Fab fragment. E and F are the heavy and light chain of a Fab fragment.

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Components

#1: Protein Voltage-gated ClC-type chloride channel eriC


Mass: 49657.711 Da / Num. of mol.: 2 / Mutation: E148Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ERIC OR B0155 / Plasmid: pet28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P37019
#2: Antibody Fab fragment (Heavy chain)


Mass: 23823.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma Cell line / References: UniProt: P01808*PLUS
#3: Antibody Fab fragment (Light chain)


Mass: 23088.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma Cell line / References: UniProt: P01837*PLUS
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: PEG 300, sodium chloride, glycine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128-31 %PEG3001reservoir
250 mMglycine1reservoirpH9.5
3100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→35 Å / Num. all: 43078 / Num. obs: 41743 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.6
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.1 / % possible all: 93.2
Reflection
*PLUS
Lowest resolution: 35 Å
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTT

1ott


Resolution: 3.3→24.85 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.325 2004 4.9 %RANDOM
Rwork0.294 ---
all0.294 42514 --
obs0.294 41239 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.19975 e/Å3
Displacement parametersBiso mean: 79.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.57 Å20 Å22.53 Å2
2--37.03 Å20 Å2
3----22.47 Å2
Refine analyzeLuzzati coordinate error free: 0.65 Å / Luzzati sigma a free: 0.98 Å
Refinement stepCycle: LAST / Resolution: 3.3→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 6 0 13229
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.622
X-RAY DIFFRACTIONc_mcangle_it2.722.5
X-RAY DIFFRACTIONc_scbond_it2.072.5
X-RAY DIFFRACTIONc_scangle_it3.343.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.495 345 5.1 %
Rwork0.454 6369 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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