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Yorodumi- PDB-5thi: Crystal Structure of 2-hydroxycyclohepta-2,4,6-trien-1-one bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5thi | ||||||
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Title | Crystal Structure of 2-hydroxycyclohepta-2,4,6-trien-1-one 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: 1.5 Å | ||||||
Authors | Dick, B. / Cohen, S. | ||||||
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 | 5thi.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5thi.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 5thi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5thi_validation.pdf.gz | 786.6 KB | Display | wwPDB validaton report |
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Full document | 5thi_full_validation.pdf.gz | 790.9 KB | Display | |
Data in XML | 5thi_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5thi_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/5thi ftp://data.pdbj.org/pub/pdb/validation_reports/th/5thi | HTTPS FTP |
-Related structure data
Related structure data | 5th4C 5thjC 5thnC 5ti0C 3ks3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
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-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: 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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-Non-polymers , 6 types, 213 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-0TR / | ||
#4: Chemical | ChemComp-CIT / | ||
#5: Chemical | ChemComp-MBO / | ||
#6: Chemical | #7: 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: 41.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / 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: Jul 20, 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: 1.5→69.54 Å / Num. obs: 38528 / % possible obs: 99.5 % / Redundancy: 5.09 % / Rmerge(I) obs: 0.0538 / Net I/σ(I): 12.87 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4379 / Num. unique all: 1376 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.491 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / 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: 13.693 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→40 Å
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