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- PDB-2exy: Crystal structure of the E148Q Mutant of EcClC, Fab complexed in ... -

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Basic information

Entry
Database: PDB / ID: 2exy
TitleCrystal structure of the E148Q Mutant of EcClC, Fab complexed in absence of bound ions
Components
  • Fab Fragment (Heavy Chain)
  • Fab Fragment (Light Chain)
  • H(+)/Cl(-) exchange transporter clcA
KeywordsMEMBRANE PROTEIN / ClC family of channels and transporters / H+/Cl- antiporter / membrane protein-Fab complex
Function / homology
Function and homology information


cellular stress response to acidic pH / chloride:proton antiporter activity / voltage-gated chloride channel activity / immunoglobulin complex / proton transmembrane transport / chloride transmembrane transport / adaptive immune response / 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 ...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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ig heavy chain V region T601 / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLobet, S. / Dutzler, R.
CitationJournal: Embo J. / Year: 2006
Title: Ion-binding properties of the ClC chloride selectivity filter.
Authors: Lobet, S. / Dutzler, R.
History
DepositionNov 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter clcA
B: H(+)/Cl(-) exchange transporter clcA
C: Fab Fragment (Heavy Chain)
D: Fab Fragment (Light Chain)
E: Fab Fragment (Heavy Chain)
F: Fab Fragment (Light Chain)


Theoretical massNumber of molelcules
Total (without water)194,6026
Polymers194,6026
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.640, 119.788, 151.300
Angle α, β, γ (deg.)90.00, 128.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H(+)/Cl(-) exchange transporter clcA / ClC-ec1


Mass: 50389.418 Da / Num. of mol.: 2 / Mutation: E148Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / 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
Has protein modificationY

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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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: peg 200/300 1:2, 150mM Tart, 50mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.919998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2004
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919998 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 59808 / Num. obs: 58313 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 89.2 Å2
Reflection shellResolution: 3.05→3.16 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OTU

1otu


Resolution: 3.1→19.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2651849.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.352 2591 4.8 %OTHER
Rwork0.328 ---
obs0.328 53513 95.6 %-
all-55976 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.244759 e/Å3
Displacement parametersBiso mean: 77.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.26 Å20 Å2-2.3 Å2
2--36.77 Å20 Å2
3----31.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.73 Å0.71 Å
Luzzati d res low-5 Å
Luzzati sigma a1.11 Å1.12 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13225 0 0 0 13225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.495 405 4.7 %
Rwork0.509 8191 -
obs--92.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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