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Yorodumi- PDB-5t74: Human carboanhydrase F131C_C206S double mutant in complex with 14 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t74 | ||||||
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Title | Human carboanhydrase F131C_C206S double mutant in complex with 14 | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | TRANSFERASE / photopharmacology / carbonic anhydrase / photochromic tethered ligand / azobenzene / computational screening | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | DuBay, K.H. / Iwan, K. / Osorio-Planes, L. / Geissler, P. / Groll, M. / Trauner, D. / Broichhagen, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: A Predictive Approach for the Optical Control of Carbonic Anhydrase II Activity. Authors: DuBay, K.H. / Iwan, K. / Osorio-Planes, L. / Geissler, P.L. / Groll, M. / Trauner, D. / Broichhagen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t74.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t74.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 5t74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t74_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5t74_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5t74_validation.xml.gz | 16 KB | Display | |
Data in CIF | 5t74_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/5t74 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/5t74 | HTTPS FTP |
-Related structure data
Related structure data | 5t71C 5t72C 5t75C 2vvaS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29228.965 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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-Non-polymers , 5 types, 373 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-HGB / |
#4: Chemical | ChemComp-75Y / |
#5: Chemical | ChemComp-TRS / |
#6: 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: 41.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3 M (NH4)2SO4, 50 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→15 Å / Num. obs: 73965 / % possible obs: 97.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.2→1.3 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 5.3 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VVA Resolution: 1.2→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.045 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.039 / 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: 13.24 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→15 Å
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