+Open data
-Basic information
Entry | Database: PDB / ID: 8q0c | ||||||
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Title | Human carbonic anhydrase II containing 3-fluorotyrosine | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Human carbonic anhydrase II / hCAII / 5-fluorotryptophane / in-cell NMR | ||||||
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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Pham, L.B.T. / Costantino, A. / Barbieri, L. / Calderone, V. / Luchinat, E. / Banci, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Controlling the incorporation of fluorinated amino acids in human cells and its structural impact. Authors: Costantino, A. / Pham, L.B.T. / Barbieri, L. / Calderone, V. / Ben-Nissan, G. / Sharon, M. / Banci, L. / Luchinat, E. #1: Journal: J Am Chem Soc / Year: 2023 Title: Direct Expression of Fluorinated Proteins in Human Cells for Authors: Pham, L.B.T. / Costantino, A. / Barbieri, L. / Calderone, V. / Luchinat, E. / Banci, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q0c.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q0c.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 8q0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q0c_validation.pdf.gz | 807.6 KB | Display | wwPDB validaton report |
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Full document | 8q0c_full_validation.pdf.gz | 811.2 KB | Display | |
Data in XML | 8q0c_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8q0c_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/8q0c ftp://data.pdbj.org/pub/pdb/validation_reports/q0/8q0c | HTTPS FTP |
-Related structure data
Related structure data | 8p6uC 8phlC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29214.707 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) References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MBO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.9M Ammonium sulfate, 0.1M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Apr 7, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→23.01 Å / Num. obs: 112511 / % possible obs: 99.46 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4638 / CC1/2: 0.4 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→23.01 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→23.01 Å
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Refine LS restraints |
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LS refinement shell |
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