+Open data
-Basic information
Entry | Database: PDB / ID: 8phl | ||||||
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Title | Human carbonic anhydrase II containing 4-fluorophenylalanine | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / hCAII / carbonic anhydrase / 4-fluorophenylalanine | ||||||
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 | 8phl.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8phl.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 8phl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8phl_validation.pdf.gz | 861.2 KB | Display | wwPDB validaton report |
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Full document | 8phl_full_validation.pdf.gz | 858.7 KB | Display | |
Data in XML | 8phl_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8phl_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/8phl ftp://data.pdbj.org/pub/pdb/validation_reports/ph/8phl | HTTPS FTP |
-Related structure data
Related structure data | 8p6uC 8q0cC 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: 29286.672 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-MBO / |
#3: Chemical | ChemComp-ZN / |
#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 Å3/Da / Density % sol: 38.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.9 Ammonium sulfate |
-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: 1.541 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Feb 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→31.5 Å / Num. obs: 57104 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.3→1.33 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4105 / CC1/2: 0.64 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.85 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.147 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→31.5 Å
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