+Open data
-Basic information
Entry | Database: PDB / ID: 1bv3 | ||||||
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Title | HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH UREA | ||||||
Components | PROTEIN (CARBONIC ANHYDRASE II) | ||||||
Keywords | LYASE / CARBONATE HYDRO-LYASE | ||||||
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 / OTHER / Resolution: 1.85 Å | ||||||
Authors | Briganti, F. / Mangani, S. / Scozzafava, A. / Vernaglione, G. / Supuran, C.T. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1999 Title: Carbonic anhydrase catalyzes cyanamide hydration to urea: is it mimicking the physiological reaction? Authors: Briganti, F. / Mangani, S. / 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 | 1bv3.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bv3.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bv3 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bv3 | 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
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: ERYTHROCYTES / 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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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HGB / |
#4: Chemical | ChemComp-URE / |
#5: 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: 2.18 Å3/Da / Density % sol: 43.6 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.7 Details: 2.3M AMMONIUM SULFATE, 55MM TRIS-HCL, 1MM SODIUM 4-(HYDROXYMERCURY)BENZOATE, PH 7, pH 7.7 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of enzyme and reservoir solutions PH range low: 7.8 / PH range high: 7.7 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: CCD / Date: May 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: GOBEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 21668 / % possible obs: 91.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 4.8 / % possible all: 92.5 |
Reflection | *PLUS Num. measured all: 55987 |
Reflection shell | *PLUS % possible obs: 92.5 % / Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.85→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE SIDE CHAIN OF HIS A 64 IS DISORDERED WITH AN OCCUPANCY OF 0.70.
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Refine analyze | Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CCP4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |