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Yorodumi- PDB-2yv7: Crystal structure of the CLIC homolog from drosophila melanogaster -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yv7 | ||||||
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Title | Crystal structure of the CLIC homolog from drosophila melanogaster | ||||||
Components | CG10997-PA | ||||||
Keywords | METAL TRANSPORT / CLIC / DmCLIC / CHLORIDE ION CHANNEL / GST FOLD | ||||||
Function / homology | Function and homology information negative gravitaxis / response to alcohol / glutathione peroxidase / glutathione peroxidase activity / chloride transport / chloride channel activity / lipid binding / calcium ion binding / mitochondrion / nucleoplasm ...negative gravitaxis / response to alcohol / glutathione peroxidase / glutathione peroxidase activity / chloride transport / chloride channel activity / lipid binding / calcium ion binding / mitochondrion / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 2yv7.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yv7.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 2yv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yv7 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yv7 | HTTPS FTP |
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-Related structure data
Related structure data | 2yv9C 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: 30208.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VY78 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-IOD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20% PEG 3350, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 26, 2005 |
Radiation | Monochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→57.07 Å / Num. obs: 29963 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.233 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K0M Resolution: 1.7→32 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.088 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.115 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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