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Yorodumi- PDB-2ht4: Structure of the Escherichia coli ClC chloride channel Y445W muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ht4 | ||||||
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Title | Structure of the Escherichia coli ClC chloride channel Y445W mutant and Fab complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ClC family of channel and transporters / H+/Cl- antiporter / Fab complex | ||||||
Function / homology | Function and homology information chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex, circulating / chloride transmembrane transport / immunoglobulin receptor binding / proton transmembrane transport / complement activation, classical pathway / antigen binding / antibacterial humoral response ...chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex, circulating / chloride transmembrane transport / immunoglobulin receptor binding / proton transmembrane transport / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / 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: 3.2 Å | ||||||
Authors | Accardi, A. / Lobet, S. / Williams, C. / Miller, C. / Dutzler, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Synergism Between Halide Binding and Proton Transport in a CLC-type Exchanger. Authors: Accardi, A. / Lobet, S. / Williams, C. / Miller, C. / Dutzler, R. | ||||||
History |
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Remark 600 | HETEROGEN EACH SUBUNIT OF THE MUTANT HAS TWO BR- IONS BOUND IN THE SELECTIVITY FILTER |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ht4.cif.gz | 332.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ht4.ent.gz | 277.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ht4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ht4_validation.pdf.gz | 483.6 KB | Display | wwPDB validaton report |
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Full document | 2ht4_full_validation.pdf.gz | 553.8 KB | Display | |
Data in XML | 2ht4_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 2ht4_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/2ht4 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2ht4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 18 - 458 / Label seq-ID: 18 - 458
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-Components
#1: Protein | Mass: 50413.441 Da / Num. of mol.: 2 / Mutation: Y445W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Plasmid: Pet 28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P37019 #2: Antibody | Mass: 23693.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA CELL LINE / References: UniProt: Q4VBH1*PLUS #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: 3.81 Å3/Da / Density % sol: 67.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 28% peg 300 v/v, 50 mM HEPES, 100mM NaBr, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9193 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2006 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9193 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. all: 46850 / Num. obs: 45398 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 69.14 Å2 / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 3.2→3.4 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / ESU R: 0.458 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.503 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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