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- PDB-6ada: Crystal structure of the E148D mutant CLC-ec1 in 200mM bromide -

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Basic information

Entry
Database: PDB / ID: 6ada
TitleCrystal structure of the E148D mutant CLC-ec1 in 200mM 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: 3.153 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)232.409, 99.956, 170.811
Angle α, β, γ (deg.)90.000, 131.880, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 30 through 450)
21(chain B and resid 30 through 450)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 30 - 450 / Label seq-ID: 30 - 450

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 30 through 450)AA
2(chain B and resid 30 through 450)BB

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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: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG400 26%(w/v), 100mM tris-SO4, 200mM NaBr

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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: 3.15→50 Å / Num. obs: 98122 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 87.47 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9800 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ENE

4ene


Resolution: 3.153→33.969 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 33.23
RfactorNum. reflection% reflection
Rfree0.2897 4865 4.96 %
Rwork0.2307 --
obs0.2336 98022 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.05 Å2 / Biso mean: 92.4991 Å2 / Biso min: 46.85 Å2
Refinement stepCycle: final / Resolution: 3.153→33.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13241 0 4 0 13245
Biso mean--165.63 --
Num. residues----1751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2550X-RAY DIFFRACTION1.487TORSIONAL
12B2550X-RAY DIFFRACTION1.487TORSIONAL
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 (%)
3.153-3.18880.47881560.40292976313295
3.1888-3.22630.38111470.373731663313100
3.2263-3.26560.43571560.364230673223100
3.2656-3.30690.42111810.352930403221100
3.3069-3.35030.44081960.336231573353100
3.3503-3.39620.36181590.32663089324899
3.3962-3.44470.36892090.316830993308100
3.4447-3.4960.39831180.283531173235100
3.496-3.55060.34691170.294231463263100
3.5506-3.60880.37911230.288531743297100
3.6088-3.67090.35831680.293831053273100
3.6709-3.73760.36681440.279131153259100
3.7376-3.80940.29781400.271831933333100
3.8094-3.8870.32041140.27931453259100
3.887-3.97140.3381820.265630953277100
3.9714-4.06370.37451640.26630943258100
4.0637-4.16510.30271180.24431683286100
4.1651-4.27750.2871880.220930823270100
4.2775-4.40310.27662040.203731173321100
4.4031-4.54490.25932040.20630763280100
4.5449-4.7070.2721810.196331093290100
4.707-4.89490.27681830.180230743257100
4.8949-5.1170.22311870.19730713258100
5.117-5.38580.23291940.178730863280100
5.3858-5.72170.26091820.185331233305100
5.7217-6.16110.24461160.194231563272100
6.1611-6.77660.23851720.1931273299100
6.7766-7.74710.20551950.171530453240100
7.7471-9.72240.22031240.16483161328599
9.7224-33.97050.29341430.23672984312795

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