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Yorodumi- PDB-3d93: Apo Human carbonic anhydrase II bound with substrate carbon dioxide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d93 | ||||||
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Title | Apo Human carbonic anhydrase II bound with substrate carbon dioxide | ||||||
Components | carbonic anhydrase IICarbonic anhydrase | ||||||
Keywords | LYASE / zinc metalloenzyme / substrate-bound / Disease mutation / Metal-binding | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Domsic, J.F. / Avvaru, B.S. / McKenna, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Entrapment of carbon dioxide in the active site of carbonic anhydrase II Authors: Domsic, J.F. / Avvaru, B.S. / Kim, C.U. / Gruner, S.M. / 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 | 3d93.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d93.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d93 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d93 | HTTPS FTP |
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-Related structure data
Related structure data | 3d92C 2cbaS S: Starting model for refinement 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00918, carbonic anhydrase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 1.3 M Ammonium citrate, 100 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→20 Å / Num. obs: 91517 / % possible obs: 93.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Χ2: 1.753 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CBA Resolution: 1.1→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: NONE | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.715 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.12 Å / % reflection obs: 89.7 % |