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Yorodumi- PDB-2d4z: Crystal structure of the cytoplasmic domain of the chloride chann... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d4z | ||||||
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Title | Crystal structure of the cytoplasmic domain of the chloride channel ClC-0 | ||||||
Components | Chloride channel protein | ||||||
Keywords | TRANSPORT PROTEIN / ClC chloride channel cytoplasmic domain / CBS domains / ion channel regulatory subunit | ||||||
Function / homology | Function and homology information voltage-gated chloride channel activity / regulation of monoatomic ion transmembrane transport / chloride channel complex Similarity search - Function | ||||||
Biological species | Torpedo marmorata (marbled electric ray) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.1 Å | ||||||
Authors | Dutzler, R. / Meyer, S. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Crystal structure of the cytoplasmic domain of the chloride channel ClC-0. Authors: Meyer, S. / Dutzler, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d4z.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4z.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d4z_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 2d4z_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 2d4z_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 2d4z_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4z ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4z | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is probably a dimer. The crystal does not contain the biological assembly. |
-Components
#1: Protein | Mass: 27786.834 Da / Num. of mol.: 2 / Fragment: ClC-0 cytoplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Torpedo marmorata (marbled electric ray) Plasmid: pET28 b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P21564 |
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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 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 3.5M sodium formate 10mM magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.919 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 12312 / Num. obs: 12275 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 72.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1200 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3.1→19.89 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1454756.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THE STRUCTURE INCLUDES STRETCHES OF WEAK ELECTRON DENSITY WITH ILL DEFINED SIDECHAINS. PARTS OF THE N-TERMINUS AS WELL AS A LINKER REGION HAVE BEEN TRACED AS A POLYGLYCINE CHAIN THEREFORE ...Details: THE STRUCTURE INCLUDES STRETCHES OF WEAK ELECTRON DENSITY WITH ILL DEFINED SIDECHAINS. PARTS OF THE N-TERMINUS AS WELL AS A LINKER REGION HAVE BEEN TRACED AS A POLYGLYCINE CHAIN THEREFORE THESE RESIDUES ARE MISSING ATOMS. SEE REMARK 470. SUBSTANTIAL PARTS OF THE LINKER SHOW NO DEFINED ELECTRON DENSITY; SEE REMARK 465.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9256 Å2 / ksol: 0.291994 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |