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Yorodumi- PDB-6lsc: Structure of the E202Y mutant of the Cl-/H+ antiporter CLC-ec1 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lsc | |||||||||
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Title | Structure of the E202Y mutant of the Cl-/H+ antiporter CLC-ec1 from E.coli: a re-refined model of the 4FTP model | |||||||||
Components | H(+)/Cl(-) exchange transporter ClcA | |||||||||
Keywords | MEMBRANE PROTEIN / CLC chloride/proton antiporter | |||||||||
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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | |||||||||
Authors | Lim, H.H. / Shane, T. / Miller, C. | |||||||||
Citation | Journal: PLoS Biol. / Year: 2012 Title: Intracellular proton access in a Cl(-)/H(+) antiporter. Authors: Lim, H.H. / Shane, T. / Miller, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lsc.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lsc.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 6lsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lsc_validation.pdf.gz | 588.1 KB | Display | wwPDB validaton report |
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Full document | 6lsc_full_validation.pdf.gz | 599.3 KB | Display | |
Data in XML | 6lsc_validation.xml.gz | 17 KB | Display | |
Data in CIF | 6lsc_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lsc ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lsc | HTTPS FTP |
-Related structure data
Related structure data | 1otsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49692.754 Da / Num. of mol.: 1 / Mutation: E202Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: clcA, eriC, yadQ, b0155, JW5012 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P37019 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 38% PEG400, 100mM CaCl2, 100mM Glycine-NaOH, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2012 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→25 Å / Num. obs: 12142 / % possible obs: 99 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 2 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.59 / Num. unique obs: 904 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OTS Resolution: 3.21→24.43 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / SU B: 18.55 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.451 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 239.86 Å2 / Biso mean: 96.111 Å2 / Biso min: 57.73 Å2
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Refinement step | Cycle: final / Resolution: 3.21→24.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.213→3.296 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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