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- PDB-6adb: Crystal structure of the E148N mutant CLC-ec1 in 20mM bromide -

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Basic information

Entry
Database: PDB / ID: 6adb
TitleCrystal structure of the E148N mutant CLC-ec1 in 20mM 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 / Resolution: 2.692 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 13, 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)195,05312
Polymers194,5746
Non-polymers4796
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)97,5276
Polymers97,2873
Non-polymers2403
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)97,5276
Polymers97,2873
Non-polymers2403
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.897, 97.980, 170.792
Angle α, β, γ (deg.)90.000, 132.020, 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: 50375.391 Da / Num. of mol.: 2 / Mutation: E148N
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.: 6 / 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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400 22%(w/v), 100mM tris-SO4, 20mM Na/K tartrate, 20mM 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: 2.692→49.6 Å / Num. obs: 153235 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 76.67 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 34.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 15117 / % possible all: 98.1

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Processing

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

4ene


Resolution: 2.692→33.961 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 34.42
RfactorNum. reflection% reflection
Rfree0.2777 7707 5.03 %
Rwork0.237 --
obs0.239 153235 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.65 Å2 / Biso mean: 88.7206 Å2 / Biso min: 44.89 Å2
Refinement stepCycle: final / Resolution: 2.692→33.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13241 0 6 0 13247
Biso mean--139.72 --
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 (%)
2.6919-2.72250.47712120.39384238445085
2.7225-2.75450.42762990.39544693499298
2.7545-2.78810.43032810.387949585239100
2.7881-2.82340.46012620.377547735035100
2.8234-2.86050.41612450.350449385183100
2.8605-2.89970.37132130.348549895202100
2.8997-2.94110.37412860.336148565142100
2.9411-2.98490.38612560.344348785134100
2.9849-3.03160.39862980.338248125110100
3.0316-3.08120.37272510.327349165167100
3.0812-3.13430.41532240.335348815105100
3.1343-3.19130.41752300.314148935123100
3.1913-3.25260.35322510.303549085159100
3.2526-3.31890.3382590.290549795238100
3.3189-3.3910.35372460.286349065152100
3.391-3.46990.32972970.276548385135100
3.4699-3.55650.35912620.277948485110100
3.5565-3.65260.37082200.269649725192100
3.6526-3.75990.29822740.259848715145100
3.7599-3.88110.3142550.257348895144100
3.8811-4.01960.28162360.243348825118100
4.0196-4.18030.27692420.2349375179100
4.1803-4.37020.23873060.206648565162100
4.3702-4.60010.20062730.192248435116100
4.6001-4.88750.20822290.189949195148100
4.8875-5.26360.23082550.196848945149100
5.2636-5.79090.26162490.197248845133100
5.7909-6.62350.21712420.19484887512999
6.6235-8.32460.20752990.17494804510399
8.3246-33.96380.24392550.20414586484194

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