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Yorodumi- PDB-1k0m: Crystal structure of a soluble monomeric form of CLIC1 at 1.4 ang... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0m | ||||||
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Title | Crystal structure of a soluble monomeric form of CLIC1 at 1.4 angstroms | ||||||
Components | CHLORIDE INTRACELLULAR CHANNEL PROTEIN 1Chloride channel | ||||||
Keywords | METAL TRANSPORT / glutathione-S-tranferase superfamily / Chloride Ion Channel | ||||||
Function / homology | Function and homology information chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / blood microparticle / nuclear membrane ...chloride transport / chloride channel activity / brush border / chloride channel complex / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / blood microparticle / nuclear membrane / vesicle / cadherin binding / perinuclear region of cytoplasm / endoplasmic reticulum / signal transduction / mitochondrion / extracellular space / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 Å | ||||||
Authors | Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. ...Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / Campbell, T.J. / Breit, S.N. / Curmi, P.M.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution. Authors: Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / ...Authors: Harrop, S.J. / DeMaere, M.Z. / Fairlie, W.D. / Reztsova, T. / Valenzuela, S.M. / Mazzanti, M. / Tonini, R. / Qiu, M.R. / Jankova, L. / Warton, K. / Bauskin, A.R. / Wu, W.M. / Pankhurst, S. / Campbell, T.J. / Breit, S.N. / Curmi, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k0m.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0m.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0m ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | SOLUBLE MONOMERIC FORM |
-Components
#1: Protein | Mass: 26881.605 Da / Num. of mol.: 2 / Fragment: CLIC1 / Mutation: E151G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00299 #2: 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: 2.08 Å3/Da / Density % sol: 40.74 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG MME 5K, AMMONIUM SULPHATE, SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MONOCHROMATOR |
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: 1.4→87 Å / Num. all: 81905 / Num. obs: 81905 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.022 / Rsym value: 0.022 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.3 / Num. unique all: 4039 / Rsym value: 0.098 / % possible all: 94.2 |
Reflection | *PLUS Lowest resolution: 87 Å / Num. obs: 81729 / % possible obs: 94.1 % / Num. measured all: 259290 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 94 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 6.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.4→87.71 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: TLS parameters refined for the N and C domains in each monomer
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Displacement parameters | Biso mean: 10.755 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→87.71 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.4 Å / Rfactor Rfree: 0.177 / Rfactor Rwork: 0.127 / Total num. of bins used: 20 | |||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.138 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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