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Yorodumi- PDB-3dv7: Role of Hydrophilic Residues in Proton Transfer During Catalysis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dv7 | ||||||
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Title | Role of Hydrophilic Residues in Proton Transfer During Catalysis by Human Carbonic Anhydrase II (N62A) | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / hCA II / Acetylation / Cytoplasm / Disease mutation / Metal-binding / Polymorphism / Zinc | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Avvaru, B.S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Role of hydrophilic residues in proton transfer during catalysis by human carbonic anhydrase II. Authors: Zheng, J. / Avvaru, B.S. / Tu, C. / McKenna, R. / Silverman, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dv7.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dv7.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/3dv7 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/3dv7 | 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: 29114.840 Da / Num. of mol.: 1 / Mutation: N62A 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 1.3 M Sodium Citrate, 50mM Tris-HCl, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R |
Detector | Detector: IMAGE PLATE / Date: Mar 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 25972 / % possible obs: 93.8 % / Redundancy: 2.4 % / Rsym value: 0.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.04 Å
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Refinement step | Cycle: LAST / Resolution: 1.7→19.04 Å
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