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Yorodumi- PDB-3ryy: Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ryy | ||||||
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Title | Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / alpha beta | ||||||
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 / molecular replacement / Resolution: 1.16 Å | ||||||
Authors | Snyder, P.W. / Bai, S. / Heroux, A. / Whitesides, G.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase. Authors: Mecinovic, J. / Snyder, P.W. / Mirica, K.A. / Bai, S. / Mack, E.T. / Kwant, R.L. / Moustakas, D.T. / Heroux, A. / 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 | 3ryy.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ryy.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ryy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/3ryy ftp://data.pdbj.org/pub/pdb/validation_reports/ry/3ryy | HTTPS FTP |
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-Related structure data
Related structure data | 3ryjC 3ryvC 3ryxC 3ryzC 3rz0C 3rz1C 3rz5C 3rz7C 3rz8C 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: 29085.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 42.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.8 Details: 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8, vapor diffusion, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.15→40 Å / Num. obs: 80129 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→35.8 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.779 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.04 Å2 / Biso mean: 13.8258 Å2 / Biso min: 3.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→35.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.191 Å / Total num. of bins used: 20
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