+Open data
-Basic information
Entry | Database: PDB / ID: 2yv9 | ||||||
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Title | Crystal structure of the CLIC homologue EXC-4 from c. elegans | ||||||
Components | Chloride intracellular channel exc-4 | ||||||
Keywords | METAL TRANSPORT / CHLORIDE ION CHANNEL / CLIC / GST FOLD / EXC-4 | ||||||
Function / homology | Function and homology information regulation of tube size / Stimuli-sensing channels / Ion homeostasis / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / apical junction complex / chloride channel activity / epithelial cell development / plasma membrane => GO:0005886 / chloride channel complex ...regulation of tube size / Stimuli-sensing channels / Ion homeostasis / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / apical junction complex / chloride channel activity / epithelial cell development / plasma membrane => GO:0005886 / chloride channel complex / lysosome / apical plasma membrane / nucleus Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Harrop, S.J. / Littler, D.R. / Curmi, P.M.G. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Comparison of vertebrate and invertebrate CLIC proteins: The crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC Authors: Littler, D.R. / Harrop, S.J. / Brown, L.J. / Pankhurst, G.J. / Mynott, A.V. / Luciani, P. / Mandyam, R.A. / Mazzanti, M. / Tanda, S. / Berryman, M.A. / Breit, S.N. / Curmi, P.M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yv9.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yv9.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yv9 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yv9 | HTTPS FTP |
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-Related structure data
Related structure data | 2yv7C 1k0mS 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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Unit cell |
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-Components
#1: Protein | Mass: 33820.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: exc-4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WQA4 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 3350, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 24, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→16.63 Å / Num. obs: 61432 / % possible obs: 75.8 % / Observed criterion σ(I): 0 / Redundancy: 3.65 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.52 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K0M Resolution: 1.6→16.61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.882 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→16.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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