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Yorodumi- PDB-6qnl: Three dimensional structure of human carbonic anhydrase XII in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qnl | ||||||
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Title | Three dimensional structure of human carbonic anhydrase XII in complex with benzenesulfonamide | ||||||
Components | Carbonic anhydrase 12 | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 Å | ||||||
Authors | Dvinskis, E. / Leitans, J. / Tars, K. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms. Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Paketuryte, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Manakova, E. / Grazulis, S. / Tars, K. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qnl.cif.gz | 235 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qnl.ent.gz | 194.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/6qnl ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qnl | HTTPS FTP |
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-Related structure data
Related structure data | 6qn0C 6qn2C 6qn5C 6qn6C 6qutC 6r6fC 6r6jC 6r6yC 6r71C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29857.201 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Production host: Escherichia coli (E. coli) / References: UniProt: O43570, carbonic anhydrase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-J92 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.6, 31% PEG 4000, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2017 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 145188 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.623 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / Num. unique obs: 21178 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Resolution: 1.53→49.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.806 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.087 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→49.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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