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Yorodumi- PDB-1avn: HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH THE HISTAMINE ACTIVATOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avn | ||||||
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Title | HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH THE HISTAMINE ACTIVATOR | ||||||
Components | CARBONIC ANHYDRASE IICarbonic anhydrase | ||||||
Keywords | LYASE / OXO-ACID | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Briganti, F. / Mangani, S. / Orioli, P. / Scozzafava, A. / Vernaglione, G. / Supuran, C.T. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Carbonic anhydrase activators: X-ray crystallographic and spectroscopic investigations for the interaction of isozymes I and II with histamine. Authors: Briganti, F. / Mangani, S. / Orioli, P. / Scozzafava, A. / Vernaglione, G. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avn.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avn.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 1avn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avn ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH HISTAMINE / Source: (gene. exp.) Homo sapiens (human) / Cell: ERYTHROCYTES / Cell line: BL21 / Plasmid: PACA/HCA II / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 159 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-HG / |
#4: Chemical | ChemComp-AZI / |
#5: Chemical | ChemComp-HSM / |
#6: 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: 2.15 Å3/Da / Density % sol: 42.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.7 Details: HCA II CRYSTALLIZED FROM 2.3 M AMMONIUM SULFATE, 50MM TRIS-HCL, 3MM SODIUM AZIDE, PH 7.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.9 Å / Num. obs: 14777 / % possible obs: 81 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.09 / Net I/σ(I): 33.61 |
Reflection shell | Resolution: 2→2.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 10.7 / Rsym value: 0.174 / % possible all: 73 |
Reflection | *PLUS Num. measured all: 49849 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 73 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→15 Å
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Displacement parameters | Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CCP4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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