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Yorodumi- PDB-4m2v: Genetically engineered Carbonic Anhydrase IX in complex with Brin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m2v | ||||||
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Title | Genetically engineered Carbonic Anhydrase IX in complex with Brinzolamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | Lyase/Lyase Inhibitor / Carbonic Anhydrase IX mimic / Lyase-Lyase Inhibitor complex | ||||||
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: 1.718 Å | ||||||
Authors | Pinard, M.P. / Boone, C.D. / Rife, B.D. / Supuran, C.T. / Mckenna, R. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2013 Title: Structural study of interaction between brinzolamide and dorzolamide inhibition of human carbonic anhydrases. Authors: Pinard, M.A. / Boone, C.D. / Rife, B.D. / Supuran, C.T. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m2v.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m2v.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 4m2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/4m2v ftp://data.pdbj.org/pub/pdb/validation_reports/m2/4m2v | 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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Details | No Symmetry operations used |
-Components
#1: Protein | Mass: 28786.363 Da / Num. of mol.: 1 / Mutation: K9A, A65S, N67Q, E69T, I91L, F130V, K169E, L203A 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-BZ1 / (+)- |
#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: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: Drops were prepared by mixing 7 uL of the final concentrated protein (~10 mg/mL) and 3 uL of precipitant solution against 1 mL of precipitant solution. The precipitant solution conditions ...Details: Drops were prepared by mixing 7 uL of the final concentrated protein (~10 mg/mL) and 3 uL of precipitant solution against 1 mL of precipitant solution. The precipitant solution conditions varied, and consisted of 50 mM Tris-HCl (pH 7.5) and 1.6 M sodium citrate., VAPOR DIFFUSION, HANGING DROP |
-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 5, 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: 1.718→20 Å / Num. obs: 26547 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.07 Å2 |
Reflection shell | Resolution: 1.72→1.78 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.718→18.95 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9179 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 14.54 / Stereochemistry target values: ML
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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: 93.36 Å2 / Biso mean: 21.4664 Å2 / Biso min: 2.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.718→18.95 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: 9
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Refinement TLS params. | Method: refined / Origin x: -5.6538 Å / Origin y: -1.7178 Å / Origin z: 86.8109 Å
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Refinement TLS group |
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