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- PDB-6k5i: Crystal structure of the E148D/R147A/F317A mutant CLC-ec1 in the ... -

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Basic information

Entry
Database: PDB / ID: 6k5i
TitleCrystal structure of the E148D/R147A/F317A mutant CLC-ec1 in the presence of 20 mM NaBr
Components
  • Fab fragment, heavy chain
  • Fab fragment, light chain
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsMEMBRANE PROTEIN / Cl-/H+ antiporter / CLC transporter
Function / homology
Function and homology information


voltage-gated chloride channel activity / antiporter activity / 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 MS 117-3 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.022 Å
AuthorsPark, K. / Lim, H.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning19-BR-01-02 Korea, Republic Of
Ministry of Science, ICT and Future Planning2017M3C7A 1048086 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
DepositionMay 29, 2019Deposition 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 6, 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: Fab fragment, heavy chain
D: Fab fragment, light chain
E: Fab fragment, heavy chain
F: Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,4118
Polymers194,2516
Non-polymers1602
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.914, 98.826, 170.295
Angle α, β, γ (deg.)90.00, 131.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 50214.168 Da / Num. of mol.: 2 / Mutation: R147A, E148D, F317A
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Escherichia coli MS 117-3 (bacteria) / Gene: clcA, eriC, HMPREF9542_03540 / Production host: Escherichia coli (E. coli) / References: UniProt: E9TIA0
#2: Antibody Fab fragment, heavy chain


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment, light chain


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400 23% (v/v), 20 mM Na/K tartrate, 100 mM Tris-SO4

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Data collection

DiffractionMean temperature: 77.36 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.02→42.9 Å / Num. obs: 109854 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.96 / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.2
Reflection shellResolution: 3.02→3.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 5476 / CC1/2: 0.813 / % possible all: 100

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Processing

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

4ene


Resolution: 3.022→42.886 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.81
RfactorNum. reflection% reflection
Rfree0.2638 5624 5.13 %
Rwork0.2104 --
obs0.213 109736 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.022→42.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13217 0 2 0 13219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913543
X-RAY DIFFRACTIONf_angle_d1.1418444
X-RAY DIFFRACTIONf_dihedral_angle_d4.1047912
X-RAY DIFFRACTIONf_chiral_restr0.062123
X-RAY DIFFRACTIONf_plane_restr0.0082314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0222-3.05650.38621160.29943223X-RAY DIFFRACTION91
3.0565-3.09250.32732160.30043569X-RAY DIFFRACTION100
3.0925-3.13020.38022100.29493323X-RAY DIFFRACTION100
3.1302-3.16980.31112410.28383535X-RAY DIFFRACTION100
3.1698-3.21150.37731580.27033480X-RAY DIFFRACTION100
3.2115-3.25550.33231930.26443437X-RAY DIFFRACTION100
3.2555-3.3020.30041840.24733515X-RAY DIFFRACTION100
3.302-3.35120.29382050.23683461X-RAY DIFFRACTION100
3.3512-3.40360.28621890.23923550X-RAY DIFFRACTION100
3.4036-3.45940.29141640.23113422X-RAY DIFFRACTION100
3.4594-3.5190.29621800.23213501X-RAY DIFFRACTION100
3.519-3.5830.34142360.23323428X-RAY DIFFRACTION100
3.583-3.65180.31212110.24433457X-RAY DIFFRACTION100
3.6518-3.72630.33181770.23253455X-RAY DIFFRACTION100
3.7263-3.80730.31631620.23573569X-RAY DIFFRACTION100
3.8073-3.89580.33721750.23493453X-RAY DIFFRACTION100
3.8958-3.99320.2911600.22713539X-RAY DIFFRACTION100
3.9932-4.10110.31351790.2163500X-RAY DIFFRACTION100
4.1011-4.22160.23092030.20763466X-RAY DIFFRACTION100
4.2216-4.35780.24921990.19693480X-RAY DIFFRACTION100
4.3578-4.51340.24072200.19553458X-RAY DIFFRACTION100
4.5134-4.69390.26651790.18043528X-RAY DIFFRACTION100
4.6939-4.90720.22481710.17133459X-RAY DIFFRACTION100
4.9072-5.16550.22581970.17283459X-RAY DIFFRACTION100
5.1655-5.48850.24652160.18543486X-RAY DIFFRACTION100
5.4885-5.91130.22971760.1883488X-RAY DIFFRACTION100
5.9113-6.50430.24021850.18793478X-RAY DIFFRACTION100
6.5043-7.44130.23791780.17823486X-RAY DIFFRACTION100
7.4413-9.35920.18041760.16323489X-RAY DIFFRACTION100
9.3592-42.89060.25381680.23813418X-RAY DIFFRACTION97

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