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Yorodumi- PDB-2ja3: Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ja3 | ||||||
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Title | Cytoplasmic Domain of the Human Chloride Transporter ClC-5 in complex with ADP | ||||||
Components | CHLORIDE CHANNEL PROTEIN 5 | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE / CHLORIDE / TRANSPORT / CBS DOMAIN / CLC / CHLORIDE CHANNEL / DISEASE MUTATION / IONIC CHANNEL / ION TRANSPORT / TRANSMEMBRANE / CHLORIDE TRANSPORTER / 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: 3.05 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 | 2ja3.cif.gz | 205.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ja3.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ja3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ja3_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 2ja3_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 2ja3_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 2ja3_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2ja3 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2ja3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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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-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 Details: 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. Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EPITHELIUM / Organ: KIDNEY / Plasmid: PET 28 B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51795 #2: Chemical | ChemComp-ADP / Sequence details | CONSTRUCT ENCOMPASSE | |
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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: 3.19 Å3/Da / Density % sol: 61.47 % |
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Crystal grow | Details: 200 MM (NH4)2SO4, 10 MM TRIS HCL (PH 7.4) AND 18 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91924 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91924 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→27.56 Å / Num. obs: 45674 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 78.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.98 / % possible all: 64.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.05→19.83 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.845 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PREDOMINANT OLIGOMERIC STATE OF THE CLC- 5 CYTOPLASMIC DOMAIN IN SOLUTION IS A DIMER. CURRENTLY THERE IS NO EXPERIMENTAL EVIDENCE FOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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.
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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: 63.71 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→19.83 Å
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Refine LS restraints |
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