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Yorodumi- PDB-3gz0: Apo-human carbonic anhydrase II revisited: Implications of the lo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gz0 | ||||||
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Title | Apo-human carbonic anhydrase II revisited: Implications of the loss of a metal in protein structure, stability and solvent network | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Apo / carbonic anhydrase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Avvaru, B.S. / McKenna, R. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Apo-Human Carbonic Anhydrase II Revisited: Implications of the Loss of a Metal in Protein Structure, Stability, and Solvent Network . Authors: Avvaru, B.S. / Busby, S.A. / Chalmers, M.J. / Griffin, P.R. / Venkatakrishnan, B. / Agbandje-McKenna, 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 | 3gz0.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gz0.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/3gz0 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/3gz0 | HTTPS FTP |
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-Related structure data
Related structure data | 2cbaS 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: 29157.863 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 / 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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: rystals of apo-HCA II were obtained through hanging drop method. 10 ul drops of equal amounts of protein and precipitant were equilibrated against precipitant solution (1.3 M Sodium Citrate, ...Details: rystals of apo-HCA II were obtained through hanging drop method. 10 ul drops of equal amounts of protein and precipitant were equilibrated against precipitant solution (1.3 M Sodium Citrate, 100mM Tris-HCl, pH 7.0) by vapor diffusion at room temperature (~20 C). A crystal was cryoprotected by quick immersion into 20% glycerol mother liquor and flash-cooled by exposing it to a gas stream of nitrogen at 100K, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→50 Å / Num. obs: 91749 / % possible obs: 93.4 % / Redundancy: 7.1 % / Rsym value: 0.085 |
Reflection shell | Highest resolution: 1.26 Å / Redundancy: 7.1 % / Rsym value: 0.085 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CBA Resolution: 1.26→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.26→50 Å
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