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- PDB-6adc: Crystal structure of the E148A mutant CLC-ec1 in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 6adc
TitleCrystal structure of the E148A mutant CLC-ec1 in the presence of 50mM bromoacetate
Components
  • H(+)/Cl(-) exchange transporter ClcA
  • antibody Fab fragment, heavy chain
  • antibody Fab fragment, light chain
KeywordsTRANSPORT PROTEIN / CLC Cl-/H+ antiporter / intermediate structure / external glutamate
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
bromoacetic acid / H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.055 Å
AuthorsLim, H.-H. / Park, K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningKBRI Basic Research Program #18-BR-01-02 Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl-/H+antiporter.
Authors: Park, K. / Lee, B.C. / Lim, H.H.
History
DepositionJul 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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: antibody Fab fragment, heavy chain
D: antibody Fab fragment, light chain
E: antibody Fab fragment, heavy chain
F: antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1868
Polymers187,9086
Non-polymers2782
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
C: antibody Fab fragment, heavy chain
D: antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0934
Polymers93,9543
Non-polymers1391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H(+)/Cl(-) exchange transporter ClcA
E: antibody Fab fragment, heavy chain
F: antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0934
Polymers93,9543
Non-polymers1391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)233.249, 96.732, 169.779
Angle α, β, γ (deg.)90.00, 131.45, 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: 47042.754 Da / Num. of mol.: 2 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody 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
#3: Antibody 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
#4: Chemical ChemComp-BXA / bromoacetic acid


Mass: 138.948 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3BrO2
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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG400 24% (w/v), 100mM glycine, 20 mM Na/K tartrate, 50 mM bromoacetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 3.055→49.9 Å / Num. obs: 102941 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 102.39 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 32.1
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10254 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.055→34.852 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 33.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 5194 5.05 %0
Rwork0.2256 ---
obs0.2281 102810 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.055→34.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13217 0 10 0 13227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113561
X-RAY DIFFRACTIONf_angle_d1.30218460
X-RAY DIFFRACTIONf_dihedral_angle_d4.3457914
X-RAY DIFFRACTIONf_chiral_restr0.0652121
X-RAY DIFFRACTIONf_plane_restr0.0082316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0554-3.09010.4028820.41671869X-RAY DIFFRACTION55
3.0901-3.12640.49952090.42053247X-RAY DIFFRACTION99
3.1264-3.16450.44841850.38913306X-RAY DIFFRACTION99
3.1645-3.20460.47371890.37633258X-RAY DIFFRACTION99
3.2046-3.24670.36172140.35363271X-RAY DIFFRACTION99
3.2467-3.29110.43061700.34013278X-RAY DIFFRACTION99
3.2911-3.33810.35691490.34113415X-RAY DIFFRACTION99
3.3381-3.38790.38671160.3383353X-RAY DIFFRACTION99
3.3879-3.44080.34721690.32833286X-RAY DIFFRACTION99
3.4408-3.49720.36491820.29883310X-RAY DIFFRACTION99
3.4972-3.55740.40991350.30353338X-RAY DIFFRACTION99
3.5574-3.6220.43211240.28583331X-RAY DIFFRACTION99
3.622-3.69160.29642050.27193357X-RAY DIFFRACTION99
3.6916-3.76690.34241940.26243251X-RAY DIFFRACTION99
3.7669-3.84870.35621790.27343337X-RAY DIFFRACTION99
3.8487-3.93810.32051670.25633302X-RAY DIFFRACTION99
3.9381-4.03640.28211520.25073369X-RAY DIFFRACTION99
4.0364-4.14540.34511870.23693263X-RAY DIFFRACTION99
4.1454-4.26720.26471980.21393285X-RAY DIFFRACTION99
4.2672-4.40470.21212050.19433298X-RAY DIFFRACTION99
4.4047-4.56180.20661860.1883281X-RAY DIFFRACTION100
4.5618-4.7440.23932040.18923252X-RAY DIFFRACTION99
4.744-4.95930.21221570.19153360X-RAY DIFFRACTION100
4.9593-5.220.27851710.19173330X-RAY DIFFRACTION99
5.22-5.54580.29481950.19453289X-RAY DIFFRACTION100
5.5458-5.9720.24981400.19463386X-RAY DIFFRACTION100
5.972-6.56940.23751740.1933299X-RAY DIFFRACTION99
6.5694-7.51170.22012180.17983301X-RAY DIFFRACTION99
7.5117-9.43280.18581750.15733294X-RAY DIFFRACTION99
9.4328-34.85450.26341630.2233100X-RAY DIFFRACTION93

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