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Yorodumi- PDB-3s78: The origin of the hydrophobic effect in the molecular recognition... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s78 | ||||||
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Title | The origin of the hydrophobic effect in the molecular recognition of arylsulfonamides by 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 / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Snyder, P.W. / Heroux, A. / Whitesides, G.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Authors: Snyder, P.W. / Mecinovic, J. / Moustakas, D.T. / Thomas, S.W. / Harder, M. / Mack, E.T. / Lockett, M.R. / Heroux, A. / Sherman, W. / 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 | 3s78.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s78.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s78_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 3s78_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 3s78_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3s78_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/3s78 ftp://data.pdbj.org/pub/pdb/validation_reports/s7/3s78 | HTTPS FTP |
-Related structure data
Related structure data | 3s71C 3s72C 3s73C 3s74C 3s75C 3s76C 3s77C 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 29070.785 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: 2.05 Å3/Da / Density % sol: 40.1 % |
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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 | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 16439 / % possible obs: 97 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Χ2: 1.173 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 33.92 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→39.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2057 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8398 / SU B: 4.388 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1984 / SU Rfree: 0.1714 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 55.03 Å2 / Biso mean: 22.7559 Å2 / Biso min: 7.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→39.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.972→2.023 Å / Total num. of bins used: 20
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