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- PDB-6ad7: Crystal structure of the E148D mutant CLC-ec1 in 20 mM bromide -

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Basic information

Entry
Database: PDB / ID: 6ad7
TitleCrystal structure of the E148D mutant CLC-ec1 in 20 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: 2.95 Å
AuthorsLim, H.-H. / Park, K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
ministryKBRI 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)194,7368
Polymers194,5766
Non-polymers1602
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)97,3684
Polymers97,2883
Non-polymers801
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)97,3684
Polymers97,2883
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)233.181, 97.610, 170.800
Angle α, β, γ (deg.)90.000, 131.790, 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.: 2 / 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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400 19%(W/v), 100mM Tris-SO4, 20mM Na/K tartrate, 20 mM 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 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: 2.95→49.036 Å / Num. obs: 113927 / % possible obs: 96.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 74.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.2
Reflection shellResolution: 2.95→3.055 Å / Redundancy: 6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11451 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ene


Resolution: 2.95→49.036 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.91
RfactorNum. reflection% reflection
Rfree0.2694 5653 4.96 %
Rwork0.2228 --
obs0.2251 113884 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.52 Å2 / Biso mean: 72.7536 Å2 / Biso min: 28.2 Å2
Refinement stepCycle: final / Resolution: 2.95→49.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13241 0 2 0 13243
Biso mean--124.04 --
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 (%)
2.95-2.98350.42171820.35563683386598
2.9835-3.01860.40871870.33873624381197
3.0186-3.05540.33851320.32983643377596
3.0554-3.09410.3471760.32683558373495
3.0941-3.13480.3691730.33493421359491
3.1348-3.17770.36121720.3113645381795
3.1777-3.22310.37451790.31953646382598
3.2231-3.27120.39811830.30943655383898
3.2712-3.32230.35272080.29193688389698
3.3223-3.37680.35782160.28543583379998
3.3768-3.4350.30762020.26953642384498
3.435-3.49750.31662120.24313688390097
3.4975-3.56470.27641790.24253585376497
3.5647-3.63740.29651950.2553637383296
3.6374-3.71650.28011850.24533632381796
3.7165-3.80290.34561880.24823499368794
3.8029-3.8980.26421710.22853376354790
3.898-4.00330.25892150.21523562377797
4.0033-4.12110.31672480.21643623387198
4.1211-4.2540.24442170.2013702391998
4.254-4.4060.271550.18443675383098
4.406-4.58230.25151840.18063644382898
4.5823-4.79070.20762100.17523659386998
4.7907-5.0430.23681820.1783499368193
5.043-5.35860.23181980.18473517371595
5.3586-5.77170.23011610.19183752391399
5.7717-6.35150.2232110.19383676388799
6.3515-7.2680.24432030.1843604380797
7.268-9.14720.18781500.16283543369393
9.1472-49.04240.23211790.24573570374995

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