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Yorodumi- PDB-4l5v: The structural implications of the secondary CO2 binding pocket i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l5v | ||||||
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Title | The structural implications of the secondary CO2 binding pocket in human carbonic anhydrase II | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / allosteric regulation / thermostability | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Boone, C.D. / Gill, S. / McKenna, R. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2013 Title: Structural, catalytic and stabilizing consequences of aromatic cluster variants in human carbonic anhydrase II. Authors: Boone, C.D. / Gill, S. / Tu, C. / 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 | 4l5v.cif.gz | 176.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l5v.ent.gz | 141.7 KB | Display | PDB format |
PDBx/mmJSON format | 4l5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/4l5v ftp://data.pdbj.org/pub/pdb/validation_reports/l5/4l5v | HTTPS FTP |
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-Related 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: 29255.047 Da / Num. of mol.: 1 / Mutation: F226L 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 |
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#2: Chemical | ChemComp-ZN / |
#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: 41.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.4M sodium citrate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2012 |
Radiation | Monochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→20 Å / Num. all: 28174 / Num. obs: 30557 / % possible obs: 92.2 % / Biso Wilson estimate: 18.56 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→18.84 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.9177 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 14.7 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.42 Å2 / Biso mean: 22.8535 Å2 / Biso min: 6.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→18.84 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -6.1607 Å / Origin y: -1.9451 Å / Origin z: 85.8684 Å
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Refinement TLS group |
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