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Yorodumi- PDB-4ygn: NaI--Interactions between Hofmeister Anions and the Binding Pocke... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ygn | |||||||||||||||
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Title | NaI--Interactions between Hofmeister Anions and the Binding Pocket of a Protein | |||||||||||||||
Components | Carbonic anhydrase 2 | |||||||||||||||
Keywords | LYASE / Hofmeister Anions / HCAII | |||||||||||||||
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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å | |||||||||||||||
Authors | Fox, J.M. / Kang, K. / Sherman, W. / Heroux, A. / Sastry, G.M. / Baghbanzadeh, M. / Lockett, M.R. / Whitesides, G.M. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Interactions between Hofmeister Anions and the Binding Pocket of a Protein. Authors: Fox, J.M. / Kang, K. / Sherman, W. / Heroux, A. / Sastry, G.M. / Baghbanzadeh, M. / Lockett, M.R. / 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 | 4ygn.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ygn.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ygn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4ygn ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4ygn | HTTPS FTP |
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-Related 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: 28998.656 Da / Num. of mol.: 1 / Fragment: UNP residues 3-260 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 | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8 |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→50 Å / Num. obs: 59438 / % possible obs: 82.4 % / Redundancy: 2.6 % / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.23→1.25 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 4 / % possible all: 26.6 |
-Processing
Software |
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Refinement | Resolution: 1.23→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.584 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.768 Å2
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Refinement step | Cycle: 1 / Resolution: 1.23→50 Å
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Refine LS restraints |
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