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- PDB-6ad8: Crystal structure of the E148D mutant CLC-ec1 in 50 mM bromide -

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Basic information

Entry
Database: PDB / ID: 6ad8
TitleCrystal structure of the E148D mutant CLC-ec1 in 50 mM bromide
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
BROMIDE ION / 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: 3.3 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 1.3Oct 23, 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)194,89510
Polymers194,5766
Non-polymers3204
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)97,4485
Polymers97,2883
Non-polymers1602
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)97,4485
Polymers97,2883
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.440, 100.080, 172.550
Angle α, β, γ (deg.)90.000, 132.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 50376.375 Da / Num. of mol.: 2 / Mutation: E148D
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400 20%(w/v), 100mM tris-SO4, 20mM Na/K tartrate, 50mM NaBr

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 3.3→50.5 Å / Num. obs: 83063 / % possible obs: 96.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 89.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6039

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.3→50.04 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.8
RfactorNum. reflection% reflection
Rfree0.2837 4201 5.06 %
Rwork0.2273 --
obs0.23 83009 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.02 Å2 / Biso mean: 94.8018 Å2 / Biso min: 41.37 Å2
Refinement stepCycle: final / Resolution: 3.3→50.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13241 0 4 0 13245
Biso mean--146.27 --
Num. residues----1751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.33750.37611390.36672730286998
3.3375-3.37680.40361570.36512568272598
3.3768-3.41790.41061530.35822692284598
3.4179-3.46120.39681540.33412595274998
3.4612-3.50670.46641380.32872702284097
3.5067-3.55470.37971440.32992593273798
3.5547-3.60550.37441420.3172645278796
3.6055-3.65930.3651740.30452509268396
3.6593-3.71650.39451360.29862725286197
3.7165-3.77740.34621340.27922545267996
3.7774-3.84250.28451300.26882485261591
3.8425-3.91230.30421500.23992518266894
3.9123-3.98760.26941480.23912673282198
3.9876-4.06890.30431450.24642654279998
4.0689-4.15740.32541100.23452681279199
4.1574-4.2540.33431150.2272684279998
4.254-4.36030.24351270.21282673280098
4.3603-4.47820.29151220.20232674279698
4.4782-4.60980.29111490.18972654280398
4.6098-4.75850.25751770.1852616279398
4.7585-4.92850.21651270.18092608273596
4.9285-5.12560.22871240.1922508263292
5.1256-5.35860.26021780.17562558273696
5.3586-5.64080.25511340.18612722285699
5.6408-5.99360.26331010.18482719282099
5.9936-6.45550.21641560.17872637279398
6.4555-7.10350.18961300.16572672280297
7.1035-8.12770.1861190.16182497261692
8.1277-10.22560.20791380.17372672281098
10.2256-50.04570.31281500.28082599274996

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