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Yorodumi- PDB-4hew: Activity Enhancers of H64A Variant of Human Carbonic Anhydrase II... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hew | ||||||
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Title | Activity Enhancers of H64A Variant of Human Carbonic Anhydrase II Possess Multiple Binding Sites within and around the Enzyme Structure | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / hydration/dehydration / His64Ala | ||||||
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 / morphogenesis of an epithelium / regulation of intracellular pH / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6984 Å | ||||||
Authors | Aggarwal, M. / McKenna, R. | ||||||
Citation | Journal: IUCrJ / Year: 2014 Title: Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles. Authors: Aggarwal, M. / Kondeti, B. / Tu, C. / Maupin, C.M. / Silverman, D.N. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hew.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hew.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 4hew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/4hew ftp://data.pdbj.org/pub/pdb/validation_reports/he/4hew | HTTPS FTP |
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-Related structure data
Related structure data | 4heyC 4hezC 4hf3C 3ks3S C: citing same article (ref.) S: Starting model for refinement |
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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: 29221.992 Da / Num. of mol.: 1 / Mutation: H64A 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: 2.08 Å3/Da / Density % sol: 40.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; ...Details: Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2011 |
Radiation | Monochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.698→19.959 Å / Num. obs: 26325 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KS3 Resolution: 1.6984→19.959 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.236 Å2 / ksol: 0.438 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6984→19.959 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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