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Yorodumi- PDB-6fjj: Joint neutron and x-ray crystal structure of human carbonic anhyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fjj | ||||||
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Title | Joint neutron and x-ray crystal structure of human carbonic anhydrase IX mimic (saccharin). | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / joint X-ray neutron diffraction / carbonic anhydrase | ||||||
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Fisher, S.Z. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2019 Title: Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative. Authors: Koruza, K. / Mahon, B.P. / Blakeley, M.P. / Ostermann, A. / Schrader, T.E. / McKenna, R. / Knecht, W. / Fisher, S.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fjj.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fjj.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/6fjj ftp://data.pdbj.org/pub/pdb/validation_reports/fj/6fjj | HTTPS FTP |
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-Related structure data
Related structure data | 6fjiC 6gcyC 4rivS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 29200.887 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-LSA / |
#4: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.2 M sodium citrate, 100 mM Tris pH 8.5 |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 6FJJ
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Reflection shell |
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-Processing
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Refinement | SU ML: 0.1 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.33 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4riv
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Refinement step | Cycle: LAST / Resolution: 1.5→25.593 Å
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Refine LS restraints |
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LS refinement shell |
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