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- PDB-2hlf: Structure of the Escherichis coli ClC chloride channel Y445E muta... -

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Basic information

Entry
Database: PDB / ID: 2hlf
TitleStructure of the Escherichis coli ClC chloride channel Y445E mutant and Fab complex
Components
  • Fab Fragment, Heavy chain
  • Fab Fragment, Light chain
  • H(+)/Cl(-) exchange transporter clcA
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / ClC family of channels and transpoters / H+/Cl- antiporter / Fab complex
Function / homology
Function and homology information


cellular stress response to acidic pH / chloride:proton antiporter activity / voltage-gated chloride channel activity / proton transmembrane transport / chloride transmembrane transport / 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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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
BROMIDE ION / H(+)/Cl(-) exchange transporter ClcA / Ighg protein / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAccardi, A. / Lobet, S. / Williams, C. / Miller, C. / Dutzler, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Synergism Between Halide Binding and Proton Transport in a CLC-type Exchanger
Authors: Accardi, A. / Lobet, S. / Williams, C. / Miller, C. / Dutzler, R.
History
DepositionJul 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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 / 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 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,3728
Polymers188,2136
Non-polymers1602
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)232.835, 97.593, 171.541
Angle α, β, γ (deg.)90.00, 131.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 18 - 458 / Label seq-ID: 2 - 442

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 47323.969 Da / Num. of mol.: 2 / Mutation: Y445E
Source method: isolated from a genetically manipulated source
Details: Each subunit of the mutant has a single Br- ion bound in the selectivity filter
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Plasmid: pET28 / 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: 23693.918 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: Q4VBH1
#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: Q58EV6
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
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: 3.87 Å3/Da / Density % sol: 68.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 34% peg 200/300 1:2, 50mM glycin, 150mM NaBr, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91921 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 24, 2005
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91921 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 44455 / Num. obs: 42596 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 109 Å2
Reflection shellResolution: 3.3→3.42 Å / % possible all: 81.7

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTS

1ots


Resolution: 3.3→40 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.902 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.597 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.30879 2154 5.1 %other
Rwork0.28082 ---
all0.28225 43145 --
obs0.28225 40441 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 128.436 Å2
Baniso -1Baniso -2Baniso -3
1--4.2 Å20 Å2-0.2 Å2
2--5.73 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13218 0 2 0 13220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 127 -
Rwork0.378 2495 -
obs--82.5 %

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