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Yorodumi- PDB-5jgt: Human carbonic anhydrase II (F131Y/L198A) complexed with 1,3-thia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jgt | ||||||
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Title | Human carbonic anhydrase II (F131Y/L198A) complexed with 1,3-thiazole-2-sulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / anhydrase / mutant / water / hydrophobic | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Fox, J.M. / Kang, K. / Sastry, M. / Sherman, W. / Sankaran, B. / Zwart, P.H. / Whitesides, G.M. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase. Authors: Fox, J.M. / Kang, K. / Sastry, M. / Sherman, W. / Sankaran, B. / Zwart, P.H. / Whitesides, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jgt.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jgt.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 5jgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jgt ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jgt | HTTPS FTP |
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-Related structure data
Related structure data | 5jdvC 5je7C 5jegC 5jehC 5jepC 5jesC 5jg3C 5jg5C 5jgsC 3s73S 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: 29115.785 Da / Num. of mol.: 1 / Mutation: F130Y, L197A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #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: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: We soaked monoclinic crystals of HCAII with BTA by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), ...Details: We soaked monoclinic crystals of HCAII with BTA by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), and 5 mM ligand. (ii) We combined 4 uL of soaking solution and 1-2 crystals of HCAII within a drop on the surface of a reservoir cover (EasyXtal CrystalSupport, Qiagen). (iii) To a clear plastic reservoir in a 15-reservoir plate (EasyXtal, Qiagen), we added 1 mL of soaking solution (without ligand present). We attached the reservoir cover to the reservoir and left the entire setup at 4 deg C for 1 week. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→40.092 Å / Num. obs: 146912 / % possible obs: 75.8 % / Redundancy: 4.1 % / Net I/σ(I): 18.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S73 Resolution: 1.1→40.092 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→40.092 Å
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Refine LS restraints |
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LS refinement shell |
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