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Yorodumi- PDB-5ti0: Crystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ti0 | ||||||
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Title | Crystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bound to human carbonic anhydrase 2 L198G | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / Carbonic Anhydrase 2 / Complex / metalloenzyme inhibitor / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Dick, B. / Cohen, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Inorg. Chem. / Year: 2017 Title: Effect of donor atom identity on metal-binding pharmacophore coordination. Authors: Dick, B.L. / Patel, A. / McCammon, J.A. / Cohen, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ti0.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ti0.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ti0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ti0_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 5ti0_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 5ti0_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5ti0_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5ti0 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5ti0 | HTTPS FTP |
-Related structure data
Related structure data | 5th4C 5thiC 5thjC 5thnC 3ks3S 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: 29232.953 Da / Num. of mol.: 1 / Mutation: L198G 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-7CZ / | ||
#4: Chemical | #5: 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: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Ammonium Sulfate, Tris, pH 8.0 VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5478 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5478 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→69.59 Å / Num. obs: 46899 / % possible obs: 99.8 % / Redundancy: 6.32 % / Rmerge(I) obs: 0.0489 / Net I/σ(I): 14.18 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5822 / Num. unique all: 1663 / % possible all: 94.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.42→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.11 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.294 Å2
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Refinement step | Cycle: 1 / Resolution: 1.42→40 Å
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Refine LS restraints |
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