+Open data
-Basic information
Entry | Database: PDB / ID: 6adb | ||||||
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Title | Crystal structure of the E148N mutant CLC-ec1 in 20mM bromide | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / CLC Cl-/H+ antiporter / intermediate structure / external glutamate | ||||||
Function / homology | Function and homology information chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / chloride transmembrane transport / proton transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 Å | ||||||
Authors | Lim, H.-H. / Park, K. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6adb.cif.gz | 335.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6adb.ent.gz | 270.9 KB | Display | PDB format |
PDBx/mmJSON format | 6adb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/6adb ftp://data.pdbj.org/pub/pdb/validation_reports/ad/6adb | HTTPS FTP |
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-Related structure data
Related structure data | 6ad7C 6ad8C 6adaC 6adcC 6k5aC 6k5dC 6k5fC 6k5iC 4eneS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 | 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 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400 22%(w/v), 100mM tris-SO4, 20mM Na/K tartrate, 20mM NaBr |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.919 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ENE Resolution: 2.692→33.961 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 34.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 188.65 Å2 / Biso mean: 88.7206 Å2 / Biso min: 44.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.692→33.961 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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