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- PDB-6k5a: Crystal structure of the E148D/R147A/F317A mutant in presence of ... -

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Basic information

Entry
Database: PDB / ID: 6k5a
TitleCrystal structure of the E148D/R147A/F317A mutant in presence of 200 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: 3.162 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 28, 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 1.3Oct 30, 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)194,57110
Polymers194,2516
Non-polymers3204
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)232.184, 101.338, 172.074
Angle α, β, γ (deg.)90.00, 132.10, 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.: 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: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 400 25% (V/V), 200 mM NaBr 100 mM Glycine

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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 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.16→39.7 Å / Num. obs: 98471 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.2
Reflection shellResolution: 3.16→3.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4868 / CC1/2: 0.795 / % 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: 3.162→39.686 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.36
RfactorNum. reflection% reflection
Rfree0.2757 4921 5 %
Rwork0.2219 --
obs0.2245 98360 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.162→39.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13171 0 4 0 13175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113543
X-RAY DIFFRACTIONf_angle_d1.23718444
X-RAY DIFFRACTIONf_dihedral_angle_d4.2427912
X-RAY DIFFRACTIONf_chiral_restr0.0632123
X-RAY DIFFRACTIONf_plane_restr0.0082314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1617-3.19760.3771160.31182233X-RAY DIFFRACTION71
3.1976-3.23520.29521550.30253138X-RAY DIFFRACTION100
3.2352-3.27470.40571570.30453207X-RAY DIFFRACTION100
3.2747-3.31610.39291960.30633039X-RAY DIFFRACTION100
3.3161-3.35970.40571370.29613264X-RAY DIFFRACTION100
3.3597-3.40570.32461680.28453118X-RAY DIFFRACTION100
3.4057-3.45430.3291630.27683144X-RAY DIFFRACTION100
3.4543-3.50590.32221640.26063203X-RAY DIFFRACTION100
3.5059-3.56060.32291880.26683021X-RAY DIFFRACTION100
3.5606-3.6190.30561880.24953228X-RAY DIFFRACTION100
3.619-3.68130.33061880.25823039X-RAY DIFFRACTION100
3.6813-3.74820.34291970.27253197X-RAY DIFFRACTION100
3.7482-3.82030.35371660.26693119X-RAY DIFFRACTION100
3.8203-3.89820.34871570.26633170X-RAY DIFFRACTION100
3.8982-3.98290.3371320.24853176X-RAY DIFFRACTION100
3.9829-4.07540.28391690.24943159X-RAY DIFFRACTION100
4.0754-4.17720.30211730.23223122X-RAY DIFFRACTION100
4.1772-4.290.26671730.2153122X-RAY DIFFRACTION100
4.29-4.41610.23071800.20023142X-RAY DIFFRACTION100
4.4161-4.55850.27081780.20643146X-RAY DIFFRACTION100
4.5585-4.72110.28211380.20523149X-RAY DIFFRACTION100
4.7211-4.90980.28761730.19993199X-RAY DIFFRACTION100
4.9098-5.13280.2621430.21253121X-RAY DIFFRACTION100
5.1328-5.40280.22861880.19263142X-RAY DIFFRACTION100
5.4028-5.74040.28111360.20333189X-RAY DIFFRACTION100
5.7404-6.18210.24161700.21363123X-RAY DIFFRACTION100
6.1821-6.80140.28571890.20443136X-RAY DIFFRACTION100
6.8014-7.77920.24341620.18483147X-RAY DIFFRACTION100
7.7792-9.77670.18871690.15763157X-RAY DIFFRACTION100
9.7767-39.68950.2661080.23943089X-RAY DIFFRACTION96

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