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Yorodumi- PDB-2j9l: Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j9l | ||||||
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Title | Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in complex with ATP | ||||||
Components | CHLORIDE CHANNEL PROTEIN 5 | ||||||
Keywords | ION CHANNEL / CHLORIDE CHANNEL / ION TRANSPORT / VOLTAGE-GATED CHANNEL | ||||||
Function / homology | Function and homology information renal system process / voltage-gated chloride channel activity / antiporter activity / chloride transport / monoatomic ion transmembrane transport / Stimuli-sensing channels / endocytosis / synaptic vesicle / apical part of cell / early endosome ...renal system process / voltage-gated chloride channel activity / antiporter activity / chloride transport / monoatomic ion transmembrane transport / Stimuli-sensing channels / endocytosis / synaptic vesicle / apical part of cell / early endosome / endosome membrane / Golgi membrane / lysosomal membrane / Golgi apparatus / ATP binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Meyer, S. / Savaresi, S. / Forster, I.C. / Dutzler, R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Nucleotide Recognition by the Cytoplasmic Domain of the Human Chloride Transporter Clc-5 Authors: Meyer, S. / Savaresi, S. / Forster, I.C. / Dutzler, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j9l.cif.gz | 220 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j9l.ent.gz | 180.6 KB | Display | PDB format |
PDBx/mmJSON format | 2j9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j9l_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 2j9l_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 2j9l_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 2j9l_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j9l ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j9l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Details | AUTHOR COMMENTS: THE PREDOMINANT OLIGOMERIC STATE OF THE CLC-5CYTOPLASMIC DOMAIN IN SOLUTION IS A DIMER. CURRENTLY THERE IS NOEXPERIMENTAL EVIDENCE FOR THE CORRECT DIMER ARRANGEMENT. APUTATIVE ARRANGEMENT IS THE PAIR OF CHAINS AB, CD AND EFRELATED BY TWO-FOLD SYMMETRY IN THE ASYMMETRIC UNIT. |
-Components
#1: Protein | Mass: 21076.469 Da / Num. of mol.: 6 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 571-746 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EPITHELIUM / Organ: KIDNEY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51795 #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-CL / #4: 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: 2.8 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Details: 200 MM (NH4)2SO4, 10 MM TRIS HCL (PH 7.4), 18% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9195 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 60291 / % possible obs: 95.3 % / Observed criterion σ(I): 2.2 / Redundancy: 5.2 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.23 / % possible all: 68.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.572 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.23 / ESU R: 0.351 / ESU R Free: 0.261 Stereochemistry target values: MAXIMUM LIKELIHOOD, RESTRAINED Details: HYDROGENS HAVE BEEN ADDED IN THE THE PREDOMINANT OLIGOMERIC STATE OF THE CLC-5 CYTOPLASMIC DOMAIN IN SOLUTION IS A DIMER. CURRENTLY THERE IS NO EXPERIMENTAL EVIDENCE FOR THE CORRECT DIMER ...Details: HYDROGENS HAVE BEEN ADDED IN THE THE PREDOMINANT OLIGOMERIC STATE OF THE CLC-5 CYTOPLASMIC DOMAIN IN SOLUTION IS A DIMER. CURRENTLY THERE IS NO EXPERIMENTAL EVIDENCE FOR THE CORRECT DIMER ARRANGEMENT. A PUTATIVE ARRANGEMENT IS THE PAIR OF CHAINS AB, CD AND EF RELATED BY TWO -FOLD SYMMETRY IN THE ASYMMETRIC UNIT. CHAIN F IS LESS WELL DEFINED WHEN COMPARED TO THE OTHER CHAINS. THIS IS DUE TO MISSING CRYSTAL CONTACTS AND IS REFLECTED IN PARTLY HIGH B- FACTORS.
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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